id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20291 ChimeraX bug report submission P.Yu@… "{{{ The following bug report has been submitted: Platform: macOS-15.3.1-arm64-arm-64bit ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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memory 3152K 22 =========== ======= ======= TOTAL 7.9G 5935 TOTAL, minus reserved VM space 7.6G 5935 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""96d59f4ca9b550771864c02f2f59ae35c9f3a92a"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""67648e5334a82511f4acf879"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""65a8173205d942272410674b"", ""factorPackIds"" : { ""SIRI_HOME_AUTOMATION_SERVER_FLOW_DEPRECATION"" : ""65d39fa4cb0e2417d11ce5f6"" }, ""deploymentId"" : 240000001 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow5.cxs"" Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel 2.08, shown at level 0.185, step 1, values float32 Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel 2.08, shown at level 0.356, step 1, values float32 Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown at level 1.17, step 1, values float32 Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size 128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size 128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32 Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size 128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32 Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size 128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32 Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size 128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32 Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size 128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32 Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel 2.08, shown at level 0.335, step 1, values float32 Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size 128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32 Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown at level 1.29, step 1, values float32 Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size 128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32 Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size 128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel 2.08, shown at level 0.271, step 1, values float32 Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size 128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32 Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32, shown at level 1.6, step 1, values float32 Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown at level 0.649, step 1, values float32 Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown at level 1.01, step 1, values float32 Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown at level 0.533, step 1, values float32 Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown at level 0.567, step 1, values float32 Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.134, step 1, values float32 Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.143, step 1, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32 Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 2, values float32 Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 2, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size 320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32 Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 1, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32 Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size 128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32 Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 0.0602, step 2, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32 Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831, shown at level 0.0515, step 1, values float32 Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831, shown at level 8.66, step 1, values float32 Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831, shown at level 0.0592, step 1, values float32 Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831, shown at level 9.68, step 1, values float32 Opened CS_P4_J302_sharp_flip.mrc as #48, grid size 80,80,80, pixel 3.32, shown at level 0.612, step 1, values float32 Opened CS_P4_J303_sharp_flip.mrc as #49, grid size 80,80,80, pixel 3.32, shown at level 0.575, step 1, values float32 Opened CS_P4_J304_sharp_flip.mrc as #50, grid size 80,80,80, pixel 3.32, shown at level 1.95, step 1, values float32 Opened CS_P4_J305_sharp_flip.mrc as #51, grid size 80,80,80, pixel 3.32, shown at level 0.569, step 1, values float32 Opened CS_P4_J306_sharp_flip.mrc as #52, grid size 80,80,80, pixel 3.32, shown at level 1.03, step 1, values float32 Opened CS_P4_J307_sharp_flip.mrc as #53, grid size 80,80,80, pixel 3.32, shown at level 0.417, step 1, values float32 Opened CS_P4_J308_sharp_flip.mrc as #54, grid size 80,80,80, pixel 3.32, shown at level 0.487, step 1, values float32 Opened CS_P4_J309_sharp_flip.mrc as #55, grid size 80,80,80, pixel 3.32, shown at level 0.427, step 1, values float32 Opened CS_P4_J310_sharp_flip.mrc as #56, grid size 80,80,80, pixel 3.32, shown at level 0.719, step 1, values float32 Opened CS_P4_J311_sharp_flip.mrc as #57, grid size 80,80,80, pixel 3.32, shown at level 0.525, step 1, values float32 Opened CS_P4_J323_sharp_flip.mrc as #58, grid size 320,320,320, pixel 0.831, shown at level 0.0616, step 1, values float32 Opened CS_P4_J324_map_locres_flip.mrc as #59, grid size 320,320,320, pixel 0.831, shown at level 3.69, step 1, values float32 Opened CS_P4_J329_sharp_flip.mrc as #60, grid size 320,320,320, pixel 0.831, shown at level 0.0566, step 1, values float32 Opened CS_P4_J330_locres_flip.mrc as #61, grid size 320,320,320, pixel 0.831, shown at level 9.71, step 1, values float32 Opened CS_P4_J300_sharp_flip.mrc as #62, grid size 320,320,320, pixel 0.831, shown at level 0.0575, step 1, values float32 Opened CS_P4_J301_locres_flip.mrc as #63, grid size 320,320,320, pixel 0.831, shown at level 3.95, step 1, values float32 Log from Thu May 7 21:11:39 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow3.cxs"" Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel 2.08, shown at level 0.185, step 1, values float32 Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel 2.08, shown at level 0.356, step 1, values float32 Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown at level 1.17, step 1, values float32 Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size 128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size 128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32 Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size 128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32 Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size 128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32 Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size 128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32 Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size 128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32 Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel 2.08, shown at level 0.335, step 1, values float32 Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size 128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32 Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown at level 1.29, step 1, values float32 Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size 128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32 Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size 128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel 2.08, shown at level 0.271, step 1, values float32 Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size 128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32 Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32, shown at level 1.6, step 1, values float32 Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown at level 0.649, step 1, values float32 Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown at level 1.01, step 1, values float32 Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown at level 0.533, step 1, values float32 Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown at level 0.567, step 1, values float32 Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.134, step 1, values float32 Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.143, step 1, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32 Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 2, values float32 Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 2, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size 320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32 Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 1, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32 Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size 128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32 Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 0.0602, step 2, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32 Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831, shown at level 0.0515, step 1, values float32 Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831, shown at level 8.66, step 1, values float32 Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831, shown at level 0.0592, step 1, values float32 Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831, shown at level 9.68, step 1, values float32 Opened CS_P4_J302_sharp_flip.mrc as #48, grid size 80,80,80, pixel 3.32, shown at level 0.612, step 1, values float32 Opened CS_P4_J303_sharp_flip.mrc as #49, grid size 80,80,80, pixel 3.32, shown at level 0.575, step 1, values float32 Opened CS_P4_J304_sharp_flip.mrc as #50, grid size 80,80,80, pixel 3.32, shown at level 1.95, step 1, values float32 Opened CS_P4_J305_sharp_flip.mrc as #51, grid size 80,80,80, pixel 3.32, shown at level 0.569, step 1, values float32 Opened CS_P4_J306_sharp_flip.mrc as #52, grid size 80,80,80, pixel 3.32, shown at level 1.03, step 1, values float32 Opened CS_P4_J307_sharp_flip.mrc as #53, grid size 80,80,80, pixel 3.32, shown at level 0.417, step 1, values float32 Opened CS_P4_J308_sharp_flip.mrc as #54, grid size 80,80,80, pixel 3.32, shown at level 0.487, step 1, values float32 Opened CS_P4_J309_sharp_flip.mrc as #55, grid size 80,80,80, pixel 3.32, shown at level 0.427, step 1, values float32 Opened CS_P4_J310_sharp_flip.mrc as #56, grid size 80,80,80, pixel 3.32, shown at level 0.719, step 1, values float32 Opened CS_P4_J311_sharp_flip.mrc as #57, grid size 80,80,80, pixel 3.32, shown at level 0.525, step 1, values float32 Opened CS_P4_J323_sharp_flip.mrc as #58, grid size 320,320,320, pixel 0.831, shown at level 0.0616, step 1, values float32 Opened CS_P4_J324_map_locres_flip.mrc as #59, grid size 320,320,320, pixel 0.831, shown at level 3.69, step 1, values float32 Opened CS_P4_J329_sharp_flip.mrc as #60, grid size 320,320,320, pixel 0.831, shown at level 0.0566, step 1, values float32 Opened CS_P4_J330_locres_flip.mrc as #61, grid size 320,320,320, pixel 0.831, shown at level 9.71, step 1, values float32 Log from Thu May 7 15:58:17 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260506_SA-F_B1_workflow.cxs"" Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel 2.08, shown at level 0.185, step 1, values float32 Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel 2.08, shown at level 0.356, step 1, values float32 Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown at level 1.17, step 1, values float32 Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size 128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size 128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32 Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size 128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32 Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size 128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32 Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size 128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32 Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size 128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32 Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel 2.08, shown at level 0.335, step 1, values float32 Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size 128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32 Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown at level 1.29, step 1, values float32 Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size 128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32 Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size 128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel 2.08, shown at level 0.271, step 1, values float32 Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size 128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32 Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32, shown at level 1.6, step 1, values float32 Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown at level 0.649, step 1, values float32 Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown at level 1.01, step 1, values float32 Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown at level 0.533, step 1, values float32 Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown at level 0.567, step 1, values float32 Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.134, step 1, values float32 Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.143, step 1, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32 Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 2, values float32 Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 2, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size 320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32 Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 1, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32 Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size 128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32 Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 0.0602, step 2, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32 Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831, shown at level 0.0515, step 1, values float32 Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831, shown at level 8.66, step 1, values float32 Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831, shown at level 0.0592, step 1, values float32 Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831, shown at level 9.68, step 1, values float32 Opened CS_P4_J302_sharp_flip.mrc as #48, grid size 80,80,80, pixel 3.32, shown at level 0.612, step 1, values float32 Opened CS_P4_J303_sharp_flip.mrc as #49, grid size 80,80,80, pixel 3.32, shown at level 0.575, step 1, values float32 Opened CS_P4_J304_sharp_flip.mrc as #50, grid size 80,80,80, pixel 3.32, shown at level 1.95, step 1, values float32 Opened CS_P4_J305_sharp_flip.mrc as #51, grid size 80,80,80, pixel 3.32, shown at level 0.569, step 1, values float32 Opened CS_P4_J306_sharp_flip.mrc as #52, grid size 80,80,80, pixel 3.32, shown at level 1.03, step 1, values float32 Opened CS_P4_J307_sharp_flip.mrc as #53, grid size 80,80,80, pixel 3.32, shown at level 0.417, step 1, values float32 Opened CS_P4_J308_sharp_flip.mrc as #54, grid size 80,80,80, pixel 3.32, shown at level 0.487, step 1, values float32 Opened CS_P4_J309_sharp_flip.mrc as #55, grid size 80,80,80, pixel 3.32, shown at level 0.427, step 1, values float32 Opened CS_P4_J310_sharp_flip.mrc as #56, grid size 80,80,80, pixel 3.32, shown at level 0.719, step 1, values float32 Opened CS_P4_J311_sharp_flip.mrc as #57, grid size 80,80,80, pixel 3.32, shown at level 0.525, step 1, values float32 Log from Wed May 6 15:19:28 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260505_SA-F_B1_workflow.cxs"" Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel 2.08, shown at level 0.185, step 1, values float32 Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel 2.08, shown at level 0.356, step 1, values float32 Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown at level 1.17, step 1, values float32 Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size 128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size 128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32 Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size 128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32 Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size 128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32 Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size 128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32 Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size 128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32 Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel 2.08, shown at level 0.335, step 1, values float32 Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size 128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32 Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown at level 1.29, step 1, values float32 Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size 128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32 Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size 128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel 2.08, shown at level 0.271, step 1, values float32 Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size 128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32 Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32, shown at level 1.6, step 1, values float32 Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown at level 0.649, step 1, values float32 Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown at level 1.01, step 1, values float32 Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown at level 0.533, step 1, values float32 Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown at level 0.567, step 1, values float32 Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.134, step 1, values float32 Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.143, step 1, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32 Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 2, values float32 Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 2, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size 320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32 Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 1, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32 Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size 128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32 Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 0.0602, step 2, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32 Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831, shown at level 0.0515, step 1, values float32 Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831, shown at level 8.66, step 1, values float32 Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831, shown at level 0.0592, step 1, values float32 Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831, shown at level 9.68, step 1, values float32 Log from Tue May 5 09:31:57 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260503_SA-F_B1_workflow4.cxs"" Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel 2.08, shown at level 0.185, step 1, values float32 Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel 2.08, shown at level 0.356, step 1, values float32 Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown at level 1.17, step 1, values float32 Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size 128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size 128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32 Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size 128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32 Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size 128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32 Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size 128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32 Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size 128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32 Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel 2.08, shown at level 0.335, step 1, values float32 Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size 128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32 Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown at level 1.29, step 1, values float32 Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size 128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32 Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size 128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel 2.08, shown at level 0.271, step 1, values float32 Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size 128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32 Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32, shown at level 1.6, step 1, values float32 Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown at level 0.649, step 1, values float32 Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown at level 1.01, step 1, values float32 Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown at level 0.533, step 1, values float32 Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown at level 0.567, step 1, values float32 Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.134, step 1, values float32 Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.143, step 1, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32 Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 2, values float32 Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 2, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size 320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32 Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 1, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32 Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size 128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32 Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 0.0602, step 2, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32 Log from Sun May 3 17:29:06 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J216_class_00_00122_volume_sharp.mrc"" Opened cryosparc_P4_J216_class_00_00122_volume_sharp.mrc as #1, grid size 128,128,128, pixel 2.08, shown at level 0.204, step 1, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J216_class_01_00122_volume_sharp.mrc"" Opened cryosparc_P4_J216_class_01_00122_volume_sharp.mrc as #2, grid size 128,128,128, pixel 2.08, shown at level 0.218, step 1, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J216_class_02_00122_volume_sharp.mrc"" Opened cryosparc_P4_J216_class_02_00122_volume_sharp.mrc as #3, grid size 128,128,128, pixel 2.08, shown at level 0.263, step 1, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J216_class_03_00122_volume_sharp.mrc"" Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size 128,128,128, pixel 2.08, shown at level 0.199, step 1, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J216_class_04_00122_volume_sharp.mrc"" Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size 128,128,128, pixel 2.08, shown at level 0.235, step 1, values float32 > lighting soft > set bgColor white > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!5 models > hide #!5 models > show #!4 models > volume #4 level 0.2842 > show #!3 models > hide #!4 models > volume #3 level 0.3546 > volume #3 level 0.356 > hide #!3 models > show #!1 models > show #!2 models > hide #!2 models > show #!5 models > hide #!1 models > color #1 #FCEDFF > hide #!5 models > show #!1 models > show #!2 models > hide #!1 models > show #!3 models > hide #!3 models > show #!3 models > hide #!2 models > show #!4 models > hide #!3 models > hide #!4 models > show #!5 models > hide #!5 models > show #!1 models > volume flip #1 Opened cryosparc_P4_J216_class_00_00122_volume_sharp.mrc z flip as #6, grid size 128,128,128, pixel 2.08, shown at step 1, values float32 > hide #!6 models > show #!2 models > volume flip #2 Opened cryosparc_P4_J216_class_01_00122_volume_sharp.mrc z flip as #7, grid size 128,128,128, pixel 2.08, shown at step 1, values float32 > hide #!7 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > volume flip #3 Opened cryosparc_P4_J216_class_02_00122_volume_sharp.mrc z flip as #8, grid size 128,128,128, pixel 2.08, shown at step 1, values float32 > show #!4 models > hide #!4 models > show #!5 models > hide #!8 models > hide #!5 models > close #1 > close #2 > close #3 > rename #6 CS_P4_J216_class_0_sharp_flip id #1 > save #1 CS_P4_J216_class_0_sharp_flip.mrc Cannot determine format for '#1' > save CS_P4_J216_class_0_sharp_flip.mrc #1 > rename #7 CS_P4_J216_class_1_sharp_flip id #1_sharp_flip.mrc #2 Invalid ""id"" argument: Expected an integer > rename #7 CS_P4_J216_class_1_sharp_flip id #1_sharp_flip id #2 Invalid ""id"" argument: Expected an integer > rename #7 CS_P4_J216_class_2_sharp_flip id #2 > rename #2 CS_P4_J216_class_1_sharp_flip > rename #8 CS_P4_J216_class_2_sharp_flip id #3 > save CS_P4_J216_class_1_sharp_flip.mrc #2 > save CS_P4_J216_class_2_sharp_flip.mrc #3 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260430_SA-F_B1_workflow.cxs"" > show #!1 models > show #!2 models > show #!3 models > show #!4 models > show #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!3 models > hide #!3 models > show #!4 models > hide #!5 models > hide #!4 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!5 models > show #!3 models > hide #!5 models > show #!1 models > select add #1 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,-2.4868,0,1,0,6.8233,0,0,1,22.302 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.85834,-0.51214,-0.03115,83.967,-0.50924,-0.85776,0.070198,298.29,-0.06267,-0.044391,-0.99705,270.86 Must specify one map, got 0 > fitmap #1 inMap #3 Fit map CS_P4_J216_class_0_sharp_flip.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 20952 points correlation = 0.8163, correlation about mean = 0.111, overlap = 1135 steps = 116, shift = 13.1, angle = 14.8 degrees Position of CS_P4_J216_class_0_sharp_flip.mrc (#1) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation 0.94377261 -0.32509802 0.06003771 31.40521096 -0.32212557 -0.94514622 -0.05416389 308.66342237 0.07435299 0.03177871 -0.99672551 251.62777867 Axis 0.98583616 -0.16420866 0.03409658 Axis point 0.00000000 154.16030965 128.66405805 Rotation angle (degrees) 177.50176084 Shift along axis -11.14516800 > select subtract #1 Nothing selected > hide #!3 models > hide #!1 models > show #!2 models > show #!3 models > fitmap #2 inMap #3 Fit map CS_P4_J216_class_1_sharp_flip.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 20964 points correlation = 0.8775, correlation about mean = 0.2387, overlap = 1535 steps = 72, shift = 7.04, angle = 9.35 degrees Position of CS_P4_J216_class_1_sharp_flip.mrc (#2) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation 0.99017956 0.04949629 -0.13074615 12.42570756 -0.06022022 0.99502365 -0.07938169 18.18421737 0.12616642 0.08647569 0.98823276 -19.36289944 Axis 0.51051058 -0.79077932 -0.33770846 Axis point 165.72686650 0.00000000 88.43510724 Rotation angle (degrees) 9.34870453 Shift along axis -1.49723285 > hide #!2 models > show #!4 models > fitmap #4 inMap #3 Fit map cryosparc_P4_J216_class_03_00122_volume_sharp.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 5887 points correlation = 0.7186, correlation about mean = 0.04573, overlap = 331.9 steps = 104, shift = 11.1, angle = 13.1 degrees Position of cryosparc_P4_J216_class_03_00122_volume_sharp.mrc (#4) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation 0.97455290 -0.13512397 0.17885231 -1.53434267 0.14053006 0.98991548 -0.01785084 -17.74958210 -0.17463660 0.04253071 0.98371398 30.92421506 Axis 0.13349556 0.78151692 0.60943437 Axis point 157.21397711 0.00000000 34.50744362 Rotation angle (degrees) 13.07084305 Shift along axis 4.76985279 > hide #!4 models > show #!5 models > select add #5 2 models selected > view matrix models > #5,0.70232,-0.70945,-0.058532,142.48,-0.70661,-0.70474,0.063551,312.49,-0.086337,-0.0032735,-0.99626,292.78 > fitmap #5 inMap #3 Fit map cryosparc_P4_J216_class_04_00122_volume_sharp.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 20952 points correlation = 0.896, correlation about mean = 0.3255, overlap = 1903 steps = 100, shift = 4.43, angle = 13 degrees Position of cryosparc_P4_J216_class_04_00122_volume_sharp.mrc (#5) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation 0.72688934 -0.68457986 0.05461051 119.19907428 -0.67457364 -0.72664609 -0.13013783 337.91149541 0.12877226 0.05775699 -0.98999082 252.38058253 Axis 0.92902840 -0.36668580 0.04947481 Axis point 0.00000000 185.59312596 132.22855036 Rotation angle (degrees) 174.19607958 Shift along axis -0.68154259 > select subtract #5 Nothing selected > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260430_SA-F_B1_workflow.cxs"" > hide #!5 models > show #!5 models > hide #!3 models > show #!1 models > hide #!5 models > hide #!1 models > show #!2 models > color #2 #FCEDFF > hide #!2 models > show #!4 models > color #4 #FCEDFF > hide #!4 models > show #!5 models > color #5 #FCEDFF > hide #!5 models > show #!3 models > color #5 #E9C29B > color #5 #FCEDFF > color #3 #E9C29B > ui mousemode right translate > volume #2 level 0.356 > volume #1 level 0.356 > volume #4 level 0.356 > volume #5 level 0.356 > hide #!3 models > show #!1 models > undo [Repeated 1 time(s)] > hide #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #1 level 0.1727 > volume #1 level 0.1851 > show #!2 models > hide #!1 models > volume #2 level 0.203 > show #!3 models > hide #!2 models > hide #!3 models > show #!4 models > volume #4 level 0.1532 > show #!3 models > select add #4 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #4,0.97455,-0.13512,0.17885,1.3208,0.14053,0.98992,-0.017851,-10.868,-0.17464,0.042531,0.98371,31.337 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.085498,-0.64922,0.75578,120.23,0.99605,-0.074063,0.049058,8.8958,0.024125,0.75698,0.65299,-39.323 > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.085498,-0.64922,0.75578,134.23,0.99605,-0.074063,0.049058,6.1939,0.024125,0.75698,0.65299,-87.477 > view matrix models > #4,-0.085498,-0.64922,0.75578,134.33,0.99605,-0.074063,0.049058,6.22,0.024125,0.75698,0.65299,-87.742 > view matrix models > #4,-0.085498,-0.64922,0.75578,130.4,0.99605,-0.074063,0.049058,5.0583,0.024125,0.75698,0.65299,-76.883 > fitmap #4 inMap #3 Fit map cryosparc_P4_J216_class_03_00122_volume_sharp.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 42435 points correlation = 0.7796, correlation about mean = 0.1614, overlap = 1558 steps = 228, shift = 2.07, angle = 23.4 degrees Position of cryosparc_P4_J216_class_03_00122_volume_sharp.mrc (#4) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation -0.31733316 -0.35582789 0.87902570 104.58434579 0.93180439 -0.28920783 0.21931579 18.83015631 0.17618244 0.88867618 0.42333722 -81.48445272 Axis 0.41511738 0.43588247 0.79855121 Axis point 65.64014873 66.59534740 0.00000000 Rotation angle (degrees) 126.27076538 Shift along axis -13.44699307 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.85396,0.083596,-0.51358,313.46,-0.52034,-0.13698,0.8429,94.578,0.00011363,0.98704,0.16047,-34.579 > fitmap #4 inMap #3 Fit map cryosparc_P4_J216_class_03_00122_volume_sharp.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 42435 points correlation = 0.7628, correlation about mean = 0.1138, overlap = 1507 steps = 160, shift = 8.1, angle = 11.6 degrees Position of cryosparc_P4_J216_class_03_00122_volume_sharp.mrc (#4) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation -0.75756109 0.20637267 -0.61928307 295.50473254 -0.63935005 -0.04324082 0.76769900 115.47474727 0.13165378 0.97751755 0.16470194 -51.62941296 Axis 0.18240424 -0.65282152 -0.73522293 Axis point 168.50534676 17.73009752 0.00000000 Rotation angle (degrees) 144.89006320 Shift along axis 16.47604383 > select subtract #4 Nothing selected > volume #4 level 0.3211 > hide #!3 models > volume #4 level 0.2347 > volume #4 level 0.2031 > hide #!4 models > show #!5 models > volume #5 level 0.1924 > volume #5 level 0.2064 > ui mousemode right translate > show #!3 models > hide #!5 models > color #3 #B9DBD5 > hide #!3 models > show #!1 models > lighting shadows true intensity 0.5 > lighting flat > graphics silhouettes false > graphics silhouettes true > lighting soft > save P4_J216_class_0_sharp.png supersample 3 transparentBackground true > hide #!1 models > show #!2 models > save P4_J216_class_1_sharp.png supersample 3 transparentBackground true > hide #!2 models > show #!3 models > save P4_J216_class_2_sharp.png supersample 3 transparentBackground true > hide #!3 models > show #!4 models > save P4_J216_class_3_sharp.png supersample 3 transparentBackground true > hide #!4 models > show #!5 models > show #!1 models > show #!2 models > show #!3 models > show #!4 models > hide #!4 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!1 models > view name P1 [Repeated 1 time(s)] > save P4_J216_class_0_sharp.png supersample 3 transparentBackground true > hide #!1 models > show #!2 models > save P4_J216_class_1_sharp.png supersample 3 transparentBackground true > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!3 models > save P4_J216_class_2_sharp.png supersample 3 transparentBackground true > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!4 models > save P4_J216_class_3_sharp.png supersample 3 transparentBackground true > hide #!4 models > show #!5 models > vieww P1 Unknown command: vieww P1 > view P1 [Repeated 1 time(s)] > save P4_J216_class_4_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260430_SA-F_B1_workflow.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J219_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J219_002_volume_map_sharp.mrc as #6, grid size 80,80,80, pixel 3.32, shown at level 0.854, step 1, values float32 > hide #!5 models > show #!3 models > select add #6 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.50968,-0.8597,0.033732,182.49,-0.85693,-0.50376,0.10903,313.05,-0.076743,-0.084479,-0.99347,263.76 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.50968,-0.8597,0.033732,181.37,-0.85693,-0.50376,0.10903,307.2,-0.076743,-0.084479,-0.99347,286.3 > fitmap #6 inMap #3 Fit map cryosparc_P4_J219_002_volume_map_sharp.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 5120 points correlation = 0.7368, correlation about mean = 0.07448, overlap = 1741 steps = 88, shift = 8.42, angle = 12.4 degrees Position of cryosparc_P4_J219_002_volume_map_sharp.mrc (#6) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation 0.68179907 -0.73031354 0.04233404 134.55628275 -0.72995927 -0.67538450 0.10495351 308.10402853 -0.04805721 -0.10245933 -0.99357566 283.32032359 Axis -0.91672636 0.39951261 0.00156579 Axis point 0.00000000 192.14085888 132.24148806 Rotation angle (degrees) 173.50439997 Shift along axis 0.18377410 > volume #6 level 1.828 > select subtract #6 Nothing selected > hide #!3 models > volume #6 level 1.172 > show #!3 models > select add #6 2 models selected > view matrix models > #6,0.6818,-0.73031,0.042334,145.51,-0.72996,-0.67538,0.10495,294.75,-0.048057,-0.10246,-0.99358,285.84 > view matrix models > #6,0.6818,-0.73031,0.042334,133.79,-0.72996,-0.67538,0.10495,309.04,-0.048057,-0.10246,-0.99358,282.76 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.47143,0.87224,0.13024,-67.58,0.87592,-0.44591,-0.18423,88.863,-0.10262,0.20093,-0.97422,246.36 > fitmap #6 inMap #3 Fit map cryosparc_P4_J219_002_volume_map_sharp.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 3507 points correlation = 0.7523, correlation about mean = 0.053, overlap = 1436 steps = 84, shift = 11, angle = 9.96 degrees Position of cryosparc_P4_J219_002_volume_map_sharp.mrc (#6) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation 0.31271016 0.94213099 0.12083688 -48.05138587 0.94223385 -0.29160641 -0.16480619 65.68302492 -0.12003221 0.16539317 -0.97889599 255.74245569 Axis 0.80789250 0.58932983 0.00025166 Axis point 0.00000000 34.02227920 132.07845223 Rotation angle (degrees) 168.20805262 Shift along axis -0.04702893 > select subtract #6 Nothing selected > hide #!6 models > show #!6 models > select add #6 2 models selected > view matrix models > #6,-0.96774,-0.18791,0.16785,278.55,-0.18769,0.98208,0.017294,25.636,-0.16809,-0.014768,-0.98566,287.91 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.96774,-0.18791,0.16785,272.6,-0.18769,0.98208,0.017294,32.876,-0.16809,-0.014768,-0.98566,284.26 > fitmap #6 inMap #3 Fit map cryosparc_P4_J219_002_volume_map_sharp.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 3507 points correlation = 0.7248, correlation about mean = 0.05418, overlap = 1264 steps = 60, shift = 9.72, angle = 10.6 degrees Position of cryosparc_P4_J219_002_volume_map_sharp.mrc (#6) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation -0.92647017 -0.30027989 0.22690311 266.55888821 -0.26721766 0.94935570 0.16528304 28.41095713 -0.26504293 0.09249729 -0.95978982 282.00607809 Axis -0.14603906 0.98705219 0.06633684 Axis point 153.43261550 0.00000000 122.88099835 Rotation angle (degrees) 165.56984584 Shift along axis 7.82248126 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.92785,-0.005043,0.37292,209.61,0.027742,0.99621,0.082497,-9.3167,-0.37192,0.086891,-0.92419,293.48 > fitmap #6 inMap #3 Fit map cryosparc_P4_J219_002_volume_map_sharp.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 3507 points correlation = 0.7519, correlation about mean = 0.05711, overlap = 1436 steps = 100, shift = 5.47, angle = 14.5 degrees Position of cryosparc_P4_J219_002_volume_map_sharp.mrc (#6) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation -0.92643320 -0.21423055 0.30955905 249.03084383 -0.21368345 0.97623560 0.03610312 27.35482068 -0.30993696 -0.03270052 -0.95019459 303.95121642 Axis -0.11038513 0.99388850 0.00087774 Axis point 150.47041621 0.00000000 131.94319456 Rotation angle (degrees) 161.84114382 Shift along axis -0.03486954 > select subtract #6 Nothing selected > hide #!3 models > hide #!6 models > show #!3 models > hide #!3 models > show #!6 models > volume flip #6 Opened cryosparc_P4_J219_002_volume_map_sharp.mrc z flip as #7, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #6 > rename CS_P4_J219_sharp_flip id #6 Missing or invalid ""models"" argument: invalid models specifier > rename #7 CS_P4_J219_sharp_flip id #6 > save CS_P4_J219_sharp_flip.mrc #6 > show #!3 models > select add #6 2 models selected > view matrix models > #6,0.55385,-0.83087,-0.054,184.1,0.82508,0.55638,-0.098423,-37.993,0.11182,0.009957,0.99368,-50.391 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.55385,-0.83087,-0.054,173.54,0.82508,0.55638,-0.098423,-43.189,0.11182,0.009957,0.99368,-15.893 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.43591,-0.88398,-0.16899,334.46,0.87276,-0.46105,0.1604,51.515,-0.2197,-0.077569,0.97248,45.011 > fitmap #6 inMap #3 Fit map CS_P4_J219_sharp_flip.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 3507 points correlation = 0.9414, correlation about mean = 0.4694, overlap = 2583 steps = 72, shift = 3.53, angle = 4.05 degrees Position of CS_P4_J219_sharp_flip.mrc (#6) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation -0.45821390 -0.85833568 -0.23086770 342.48607306 0.85407817 -0.49711214 0.15306861 63.33623820 -0.24615139 -0.12704090 0.96086946 56.91191433 Axis -0.16142412 0.00880783 0.98684582 Axis point 157.30567711 132.03749632 0.00000000 Rotation angle (degrees) 119.81679395 Shift along axis 1.43562700 > select subtract #6 Nothing selected > hide #!3 models Unsupported scale factor (0.000000) detected on Display1 [Repeated 2 time(s)] > hide #!6 models > show #!3 models > show #!6 models > hide #!6 models > color #3 #B1DCFC > save P4_J216_class_2_sharp.png supersample 3 transparentBackground true > hide #!3 models > show #!3 models > hide #!3 models > show #!6 models > hide #!6 models > show #!3 models > show #!6 models > hide #!3 models > hide #!6 models > show #!3 models > color #3 #AFDBFF > hide #!3 models > show #!6 models > show #!3 models > hide #!3 models > show #!3 models > hide #!6 models > show #!6 models > color #3 #99BFE5 > hide #!6 models > view P1 > save P4_J216_class_2_sharp.png supersample 3 transparentBackground true > hide #!3 models > show #!6 models > ui mousemode right translate > save P4_J219_NU_sharp_flip.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260430_SA-F_B1_workflow.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J243_003_volume_map_sharp.mrc"" Opened cryosparc_P4_J243_003_volume_map_sharp.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.1, step 1, values float32 > select add #7 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.34351,0.88804,0.30558,-69.154,0.93106,-0.36463,0.013018,61.425,0.12299,0.28005,-0.95208,168.53 > view matrix models > #7,-0.72211,0.66266,0.19859,108.59,0.68148,0.73076,0.039546,-55.441,-0.11892,0.16389,-0.97928,217.85 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.72211,0.66266,0.19859,107.8,0.68148,0.73076,0.039546,-63.119,-0.11892,0.16389,-0.97928,255.33 > view matrix models > #7,-0.72211,0.66266,0.19859,116.79,0.68148,0.73076,0.039546,-56.849,-0.11892,0.16389,-0.97928,258.31 > fitmap #7 inMap #6 Fit map cryosparc_P4_J243_003_volume_map_sharp.mrc in map CS_P4_J219_sharp_flip.mrc using 5116 points correlation = 0.9377, correlation about mean = 0.7097, overlap = 1.519e+04 steps = 76, shift = 2.16, angle = 10.6 degrees Position of cryosparc_P4_J243_003_volume_map_sharp.mrc (#7) relative to CS_P4_J219_sharp_flip.mrc (#6) coordinates: Matrix rotation and translation 0.96909604 0.16642828 0.18208375 -39.18937125 0.15922720 -0.98578684 0.05358170 236.77616183 0.18841328 -0.02293313 -0.98182203 241.04145354 Axis -0.99224103 -0.08208102 -0.09338329 Axis point 0.00000000 122.34870623 120.06626952 Rotation angle (degrees) 177.79032322 Shift along axis -3.05877231 > select subtract #7 Nothing selected > select add #7 2 models selected > view matrix models > #7,-0.62422,0.77517,0.097247,102.65,0.77737,0.62868,-0.021408,-52.876,-0.077732,0.062233,-0.99503,269.09 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.32669,-0.93485,0.13901,287.37,-0.94032,0.30667,-0.14745,222.88,0.095218,-0.17888,-0.97925,277.34 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.32669,-0.93485,0.13901,281.61,-0.94032,0.30667,-0.14745,233.21,0.095218,-0.17888,-0.97925,273.65 > fitmap #7 inMap #6 Fit map cryosparc_P4_J243_003_volume_map_sharp.mrc in map CS_P4_J219_sharp_flip.mrc using 5116 points correlation = 0.9419, correlation about mean = 0.7222, overlap = 1.551e+04 steps = 56, shift = 3.52, angle = 7.25 degrees Position of cryosparc_P4_J243_003_volume_map_sharp.mrc (#7) relative to CS_P4_J219_sharp_flip.mrc (#6) coordinates: Matrix rotation and translation -0.62645631 0.77281267 0.10155321 101.66723571 0.77509514 0.63140454 -0.02357570 -50.90352474 -0.08234076 0.06394425 -0.99455072 266.97848709 Axis 0.42971205 0.90289643 0.01120665 Axis point 70.49413903 0.00000000 130.93970837 Rotation angle (degrees) 174.15511884 Shift along axis 0.71895896 > select subtract #7 Nothing selected > hide #!6 models > volume #7 level 1.41 > color #7 #99BFE5 > view P1 > close #7 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J244_003_volume_map_sharp.mrc"" Opened cryosparc_P4_J244_003_volume_map_sharp.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.05, step 1, values float32 > show #!6 models > select add #7 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.71966,-0.6805,-0.13788,149.49,-0.69285,-0.71678,-0.078638,342.79,-0.045318,0.15212,-0.98732,223.99 > hide #!6 models > show #!6 models > ui mousemode right ""translate selected models"" > view matrix models > #7,0.71966,-0.6805,-0.13788,149.4,-0.69285,-0.71678,-0.078638,338.98,-0.045318,0.15212,-0.98732,258.19 > select subtract #7 Nothing selected > hide #!6 models > volume flip #7 Opened cryosparc_P4_J244_003_volume_map_sharp.mrc z flip as #8, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #7 > rename #8 CS_P4_J244_sharp_flip id #7 > save CS_P4_J244_sharp_flip.mrc #7 > color #7 #99BFE5 > volume #7 level 1.156 > save CS_P4_J244_sharp_flip.mrc #7 > save P4_J244_NU_sharp_flip.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J242_class_00_00122_volume_sharp.mrc"" Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size 128,128,128, pixel 2.08, shown at level 0.192, step 1, values float32 > hide #!7 models > volume #8 level 0.2208 > show #!7 models > select add #8 2 models selected > view matrix models #8,1,0,0,1.7912,0,1,0,4.218,0,0,1,1.8536 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.019063,-0.87425,-0.4851,301.31,0.055421,0.48537,-0.87255,194.56,0.99828,-0.010251,0.057705,27.748 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.019063,-0.87425,-0.4851,303.09,0.055421,0.48537,-0.87255,199.03,0.99828,-0.010251,0.057705,19.845 > view matrix models > #8,0.019063,-0.87425,-0.4851,323.73,0.055421,0.48537,-0.87255,193.31,0.99828,-0.010251,0.057705,17.439 > view matrix models > #8,0.019063,-0.87425,-0.4851,322.89,0.055421,0.48537,-0.87255,188.18,0.99828,-0.010251,0.057705,19.28 > fitmap #8 inMap #7 Fit map cryosparc_P4_J242_class_00_00122_volume_sharp.mrc in map CS_P4_J244_sharp_flip.mrc using 14754 points correlation = 0.481, correlation about mean = 0.07756, overlap = 1756 steps = 112, shift = 13.3, angle = 15.3 degrees Position of cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) relative to CS_P4_J244_sharp_flip.mrc (#7) coordinates: Matrix rotation and translation 0.05423844 -0.87969653 0.47243223 170.87663448 0.10002936 0.47553549 0.87399092 -59.90285646 -0.99350507 -0.00014682 0.11378778 232.31099922 Axis -0.44417982 0.74489379 0.49783284 Axis point 199.16697689 -0.00000000 41.59458970 Rotation angle (degrees) 100.26604714 Shift along axis -4.86917491 > select subtract #8 Nothing selected > hide #!7 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J242_class_01_00122_volume_sharp.mrc"" Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size 128,128,128, pixel 2.08, shown at level 0.178, step 1, values float32 > hide #!8 models > volume #9 level 0.1464 > show #!8 models > select add #9 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.01099,0.99675,0.079835,4.9565,0.1314,-0.080587,0.98805,-14.68,0.99127,-0.00036851,-0.13186,9.8 > ui mousemode right ""translate selected models"" > view matrix models > #9,0.01099,0.99675,0.079835,10.903,0.1314,-0.080587,0.98805,5.6709,0.99127,-0.00036851,-0.13186,51.786 > view matrix models > #9,0.01099,0.99675,0.079835,4.7224,0.1314,-0.080587,0.98805,-1.1935,0.99127,-0.00036851,-0.13186,45.788 > fitmap #9 inMap #8 Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_00_00122_volume_sharp.mrc using 29766 points correlation = 0.8496, correlation about mean = 0.3082, overlap = 1328 steps = 284, shift = 18.3, angle = 53.9 degrees Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) relative to cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) coordinates: Matrix rotation and translation 0.99575722 -0.02668322 0.08806571 -8.52134797 -0.09034177 -0.46538978 0.88048323 89.22150736 0.01749075 -0.88470354 -0.46582584 307.69453028 Axis -0.99855360 0.03992375 -0.03601119 Axis point 0.00000000 137.23273941 127.10917488 Rotation angle (degrees) 117.88699495 Shift along axis 0.99063260 > select subtract #9 Nothing selected > hide #!8 models > hide #!9 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J242_class_02_00122_volume_sharp.mrc"" Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 > select add #10 2 models selected > show #!9 models > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.17462,0.93232,0.31669,19.869,0.21917,0.35036,-0.91061,163.76,-0.95993,-0.089597,-0.26552,316.03 > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.17462,0.93232,0.31669,8.7975,0.21917,0.35036,-0.91061,193.69,-0.95993,-0.089597,-0.26552,324.3 > view matrix models > #10,-0.17462,0.93232,0.31669,5.0809,0.21917,0.35036,-0.91061,186.44,-0.95993,-0.089597,-0.26552,324.52 > fitmap #10 inMap #9 Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc using 20970 points correlation = 0.8182, correlation about mean = 0.3079, overlap = 1048 steps = 212, shift = 18, angle = 29.3 degrees Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative to cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) coordinates: Matrix rotation and translation -0.92160797 -0.37293352 0.10751436 286.70013052 -0.37621404 0.79028143 -0.48365097 141.61699812 0.09540306 -0.48618500 -0.86863249 299.79876520 Axis -0.19795503 0.94611818 -0.25626978 Axis point 158.67244900 0.00000000 168.59386356 Rotation angle (degrees) 179.63327476 Shift along axis 0.40332117 > select subtract #10 Nothing selected > hide #!9 models > hide #!10 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J242_class_03_00122_volume_sharp.mrc"" Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size 128,128,128, pixel 2.08, shown at level 0.218, step 1, values float32 > volume #11 level 0.1502 > show #!10 models > select add #11 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #11,0.73904,-0.47164,0.48101,26.135,-0.11204,0.61802,0.77814,-47.481,-0.66427,-0.62897,0.4039,253.49 > ui mousemode right ""translate selected models"" > view matrix models > #11,0.73904,-0.47164,0.48101,5.5926,-0.11204,0.61802,0.77814,-27.642,-0.66427,-0.62897,0.4039,266.06 > ui mousemode right ""rotate selected models"" > view matrix models > #11,-0.56676,0.0073102,0.82385,78.335,0.19153,-0.97139,0.14038,216.5,0.80131,0.23736,0.54915,-63.542 > select subtract #11 Nothing selected > fitmap #11 inMap #10 Fit map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 45754 points correlation = 0.7333, correlation about mean = -0.04196, overlap = 1268 steps = 132, shift = 23.8, angle = 15.3 degrees Position of cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) relative to cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates: Matrix rotation and translation -0.26691235 0.13508665 -0.95420616 300.80664915 -0.90776913 -0.36770197 0.20186745 274.07355373 -0.32359389 0.92007981 0.22077169 18.93443182 Axis 0.50771970 -0.44579332 -0.73721708 Axis point 236.02557416 49.14154001 0.00000000 Rotation angle (degrees) 134.98497404 Shift along axis 16.58651491 > hide #!10 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J242_class_04_00122_volume_sharp.mrc"" Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size 128,128,128, pixel 2.08, shown at level 0.261, step 1, values float32 > show #!10 models > hide #!10 models > select add #12 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #12,1,0,0,-3.7479,0,1,0,3.9168,0,0,1,20.991 > ui mousemode right ""rotate selected models"" > view matrix models > #12,0.79132,-0.13023,0.59737,-27.645,0.22144,0.97176,-0.081485,-12.263,-0.56989,0.19676,0.79781,93.603 > ui mousemode right ""translate selected models"" > view matrix models > #12,0.79132,-0.13023,0.59737,-50.124,0.22144,0.97176,-0.081485,3.5285,-0.56989,0.19676,0.79781,102.68 > view matrix models > #12,0.79132,-0.13023,0.59737,-48.335,0.22144,0.97176,-0.081485,2.277,-0.56989,0.19676,0.79781,101.98 > view matrix models > #12,0.79132,-0.13023,0.59737,-41.566,0.22144,0.97176,-0.081485,-1.9637,-0.56989,0.19676,0.79781,101.41 > fitmap #12 inMap #11 Fit map cryosparc_P4_J242_class_04_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc using 20956 points correlation = 0.8514, correlation about mean = 0.04285, overlap = 1430 steps = 80, shift = 7.16, angle = 11.7 degrees Position of cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) relative to cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) coordinates: Matrix rotation and translation -0.93263188 0.26201641 0.24808299 197.07280134 -0.29117819 -0.95255879 -0.08858337 308.05329962 0.21310334 -0.15485204 0.96468016 17.95641726 Axis -0.11870856 0.06265985 -0.99095006 Axis point 119.69175871 140.62215054 0.00000000 Rotation angle (degrees) 163.79210928 Shift along axis -21.88556717 > select subtract #12 Nothing selected > hide #!11 models > volume #12 level 0.4033 > volume #12 level 0.3453 > color #8 #FCEDFF > hide #!12 models > show #!8 models > hide #!8 models > show #!9 models > color #9 #FCEDFF > hide #!9 models > show #!10 models > color #10 #FCEDFF > hide #!10 models > show #!11 models > color #11 #FCEDFF > hide #!11 models > show #!12 models > color #12 #99BFE5 > view P1 > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!1 models > hide #!1 models > show #!6 models > hide #!6 models > show #!3 models > select add #12 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #12,0.95369,-0.29732,-0.045496,35.025,0.29889,0.95373,0.032695,-17.906,0.03367,-0.044779,0.99843,26.075 > view matrix models > #12,-0.8879,0.32078,-0.32974,233.6,0.30063,0.94715,0.1119,-26.299,0.34821,0.00022498,-0.93742,198.42 > ui mousemode right ""translate selected models"" > view matrix models > #12,-0.8879,0.32078,-0.32974,232.89,0.30063,0.94715,0.1119,-34.317,0.34821,0.00022498,-0.93742,213.72 > view matrix models > #12,-0.8879,0.32078,-0.32974,243.25,0.30063,0.94715,0.1119,-55.273,0.34821,0.00022498,-0.93742,214.76 > ui mousemode right ""rotate selected models"" > view matrix models > #12,-0.88731,0.39919,0.23093,169.34,0.40717,0.91324,-0.014156,-50.796,-0.21654,0.081466,-0.97287,283.71 > fitmap #12 inMap #3 Fit map cryosparc_P4_J242_class_04_00122_volume_sharp.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 12546 points correlation = 0.9893, correlation about mean = 0.7632, overlap = 2433 steps = 124, shift = 11, angle = 27.9 degrees Position of cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation -0.62359754 0.77535022 0.09979057 101.14085164 0.77719680 0.62864768 -0.02769904 -50.42984630 -0.08420957 0.06028386 -0.99462285 268.88184712 Axis 0.43136931 0.90213001 0.00905357 Axis point 70.24601107 0.00000000 131.83510298 Rotation angle (degrees) 174.14674629 Shift along axis 0.56912319 > select subtract #12 Nothing selected > hide #!12 models > show #!12 models > show #!11 models > select add #11 2 models selected > view matrix models > #11,-0.37852,0.89247,0.24538,28.817,0.88041,0.42898,-0.20213,16.101,-0.28566,0.13952,-0.94812,300.03 > ui mousemode right ""translate selected models"" > view matrix models > #11,-0.37852,0.89247,0.24538,46.8,0.88041,0.42898,-0.20213,-5.6117,-0.28566,0.13952,-0.94812,300.85 > view matrix models > #11,-0.37852,0.89247,0.24538,36.63,0.88041,0.42898,-0.20213,-16.953,-0.28566,0.13952,-0.94812,296.6 > fitmap #11 inMap #12 Fit map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_04_00122_volume_sharp.mrc using 45754 points correlation = 0.7192, correlation about mean = 0.1299, overlap = 1714 steps = 96, shift = 6.98, angle = 12.7 degrees Position of cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) relative to cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.88557701 -0.25567312 -0.38779454 99.27082409 0.32552043 0.93717068 0.12548928 -53.44589150 0.33134544 -0.23736546 0.91316364 -22.95393091 Axis -0.36530839 -0.72400286 0.58512361 Axis point 106.02252826 0.00000000 214.34257569 Rotation angle (degrees) 29.77806268 Shift along axis -11.00037360 > select subtract #11 Nothing selected > hide #!12 models > show #!12 models > hide #!12 models > hide #!3 models > show #!12 models > hide #!11 models > show #!10 models > select add #10 2 models selected > view matrix models > #10,-0.49822,0.81176,0.30466,37.524,-0.14214,0.27015,-0.95227,247.33,-0.85532,-0.51775,-0.019207,343.36 > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.013344,0.85199,0.52339,-68.961,-0.1627,-0.51831,0.83957,128.11,0.98659,-0.073951,0.14553,-15.381 > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.013344,0.85199,0.52339,-45.161,-0.1627,-0.51831,0.83957,119.13,0.98659,-0.073951,0.14553,-13.578 > fitmap #10 inMap #12 Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_04_00122_volume_sharp.mrc using 20970 points correlation = 0.7101, correlation about mean = 0.02358, overlap = 908.6 steps = 80, shift = 7.98, angle = 9.33 degrees Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative to cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.35385865 -0.88893073 0.29083707 267.80089120 -0.02210060 0.31881642 0.94755878 -31.84809054 -0.93503776 0.32887420 -0.13246184 232.75133151 Axis -0.38099533 0.75491227 0.53380711 Axis point 205.22642342 0.00000000 36.94010088 Rotation angle (degrees) 125.71487620 Shift along axis -1.82908632 > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.12287,-0.47662,0.87048,95.543,0.19038,-0.87215,-0.45067,269.26,0.97399,0.11035,0.1979,-37.789 > select subtract #10 Nothing selected > hide #!12 models > show #!11 models > show #!12 models > hide #!10 models > hide #!12 models > show #!10 models > select add #10 2 models selected > view matrix models > #10,-0.38685,-0.21971,0.89558,99.669,-0.053858,-0.96416,-0.2598,294.54,0.92057,-0.14874,0.36115,-16.709 > fitmap #10 inMap #11 Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc using 20970 points correlation = 0.8482, correlation about mean = 0.1221, overlap = 870.1 steps = 88, shift = 3.31, angle = 12.5 degrees Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative to cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) coordinates: Matrix rotation and translation -0.32110732 -0.67353914 -0.66575904 357.49560201 0.09667773 -0.72262784 0.68444314 122.97291760 -0.94209527 0.15541563 0.29715733 219.46626263 Axis -0.54292343 0.28359472 0.79044809 Axis point 234.55310205 82.20310947 0.00000000 Rotation angle (degrees) 150.84311237 Shift along axis 14.25842210 > view matrix models > #10,-0.30509,0.38504,-0.87101,233.77,0.18733,0.92101,0.34153,-54.422,0.93372,-0.058973,-0.35312,61.617 > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.30509,0.38504,-0.87101,240.35,0.18733,0.92101,0.34153,-58.712,0.93372,-0.058973,-0.35312,49.559 > view matrix models > #10,-0.30509,0.38504,-0.87101,238.16,0.18733,0.92101,0.34153,-58.03,0.93372,-0.058973,-0.35312,51.895 > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.36524,0.52001,-0.77213,217.65,0.08187,0.84416,0.5298,-55.56,0.9273,0.13029,-0.3509,28.264 > fitmap #10 inMap #11 Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc using 20970 points correlation = 0.8485, correlation about mean = 0.1929, overlap = 854.7 steps = 140, shift = 18.2, angle = 22.5 degrees Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative to cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) coordinates: Matrix rotation and translation -0.33967352 0.22689098 0.91276633 25.87088295 0.00914596 0.97121791 -0.23801704 28.63290177 -0.94049893 -0.07249996 -0.33197214 335.97765353 Axis 0.08835402 0.98928424 -0.11623361 Axis point 129.11230783 0.00000000 160.33867701 Rotation angle (degrees) 110.50039702 Shift along axis -8.44002041 > view matrix models > #10,-0.23006,0.48061,-0.84622,212.13,0.22993,0.87177,0.43261,-89.291,0.94562,-0.095042,-0.31107,58.162 > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.23006,0.48061,-0.84622,206.51,0.22993,0.87177,0.43261,-81.849,0.94562,-0.095042,-0.31107,43.385 > view matrix models > #10,-0.23006,0.48061,-0.84622,209.88,0.22993,0.87177,0.43261,-83.853,0.94562,-0.095042,-0.31107,44.292 > select subtract #10 Nothing selected > hide #!10 models > hide #!11 models > show #!10 models > hide #!10 models > show #!9 models > show #!10 models > select add #9 2 models selected > view matrix models > #9,0.18919,0.68161,-0.70683,127.56,-0.072128,0.72753,0.68227,-34.663,0.97929,-0.078095,0.1868,-5.196 > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.094504,0.99539,-0.016524,13.65,-0.46578,0.02954,-0.88441,305.71,-0.87984,0.091276,0.46642,193.56 > ui mousemode right ""translate selected models"" > view matrix models > #9,0.094504,0.99539,-0.016524,15.801,-0.46578,0.02954,-0.88441,306.87,-0.87984,0.091276,0.46642,176.78 > view matrix models > #9,0.094504,0.99539,-0.016524,12.042,-0.46578,0.02954,-0.88441,307.73,-0.87984,0.091276,0.46642,167.03 > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.21351,-0.97318,0.085687,220.62,-0.11603,0.061829,0.99132,14.069,-0.97003,-0.2216,-0.099713,290.21 > ui mousemode right ""translate selected models"" > view matrix models > #9,0.21351,-0.97318,0.085687,223.99,-0.11603,0.061829,0.99132,9.6501,-0.97003,-0.2216,-0.099713,279.71 > fitmap #9 inMap #10 Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 29766 points correlation = 0.8261, correlation about mean = 0.3518, overlap = 1268 steps = 228, shift = 10.5, angle = 43.8 degrees Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) relative to cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates: Matrix rotation and translation -0.79231406 -0.50183310 0.34698987 259.09489231 0.60835065 -0.60661249 0.51179172 70.83831660 -0.04634564 0.61659129 0.78591810 -47.09681091 Axis 0.08862868 0.33264264 0.93887903 Axis point 119.55771099 88.88471782 0.00000000 Rotation angle (degrees) 143.75577737 Shift along axis 2.30887434 > select subtract #9 Nothing selected > hide #!9 models > hide #!10 models > show #!9 models > show #!10 models > hide #!10 models > show #!8 models > hide #!9 models > show #!9 models > select add #8 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.57009,0.77789,0.26434,-76.801,0.087184,0.26265,-0.96094,232.01,-0.81694,0.57087,0.081917,150.81 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.57009,0.77789,0.26434,-65.422,0.087184,0.26265,-0.96094,221.32,-0.81694,0.57087,0.081917,140.75 > view matrix models > #8,0.57009,0.77789,0.26434,-76.259,0.087184,0.26265,-0.96094,220.33,-0.81694,0.57087,0.081917,139.28 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.35163,-0.43011,0.83148,20.753,0.096433,0.90012,0.42483,-70.009,-0.93116,-0.069204,0.35799,194.15 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.35163,-0.43011,0.83148,32.249,0.096433,0.90012,0.42483,-69.075,-0.93116,-0.069204,0.35799,199.19 > fitmap #8 inMap #9 Fit map cryosparc_P4_J242_class_00_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc using 14754 points correlation = 0.886, correlation about mean = 0.3322, overlap = 930.7 steps = 164, shift = 11.7, angle = 31.5 degrees Position of cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) relative to cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.99392076 -0.10814474 0.02064566 12.78899705 -0.02517844 -0.40582068 -0.91360584 308.93876287 0.10718010 0.90753198 -0.40607651 52.31471926 Axis 0.99784036 -0.04741407 0.04545901 Axis point 0.00000000 137.80284162 126.13315110 Rotation angle (degrees) 114.14129203 Shift along axis 0.49150880 > select subtract #8 Nothing selected > hide #!9 models > show #!9 models > hide #!8 models > show #!8 models > hide #!9 models > view P1 > show #!9 models > hide #!8 models > hide #!9 models > show #!10 models > hide #!10 models > show #!11 models > hide #!11 models > show #!12 models > hide #!12 models > show #!8 models > show #!12 models > view P1 > select add #8 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.17056,0.37082,0.91291,-61.936,0.033776,0.92374,-0.38153,50.195,-0.98477,0.095906,0.14502,217.51 > select subtract #8 Nothing selected > hide #!12 models > show #!9 models > select add #9 2 models selected > view matrix models > #9,0.22431,-0.86548,-0.44791,277.63,0.10958,-0.43431,0.89407,50.356,-0.96834,-0.24963,-0.0025846,282.76 > fitmap #9 inMap #8 Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_00_00122_volume_sharp.mrc using 29766 points correlation = 0.8496, correlation about mean = 0.3079, overlap = 1328 steps = 196, shift = 4.92, angle = 23.1 degrees Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) relative to cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) coordinates: Matrix rotation and translation 0.99577299 -0.02696715 0.08780046 -8.42294333 -0.09023986 -0.46536786 0.88050527 89.20116331 0.01711480 -0.88470646 -0.46583426 307.74421532 Axis -0.99855897 0.03998603 -0.03579261 Axis point 0.00000000 137.24012810 127.13677639 Rotation angle (degrees) 117.88604570 Shift along axis 0.96263749 > select subtract #9 Nothing selected > select add #9 2 models selected > select subtract #9 Nothing selected > hide #!8 models > hide #!9 models > show #!9 models > show #!10 models > show #!8 models > hide #!9 models > hide #!8 models > show #!9 models > select add #10 2 models selected > view matrix models > #10,-0.15057,0.45945,-0.87535,204.11,-0.21614,0.84872,0.48265,-19.059,0.96468,0.26187,-0.028487,-39.785 > fitmap #10 inMap #8 Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_00_00122_volume_sharp.mrc using 20970 points correlation = 0.8656, correlation about mean = 0.3963, overlap = 1232 steps = 148, shift = 6.34, angle = 30.8 degrees Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative to cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) coordinates: Matrix rotation and translation -0.99459983 0.06769619 -0.07866640 263.08124995 0.09074118 0.93510189 -0.34256458 42.75279763 0.05037079 -0.34785296 -0.93619501 298.73878944 Axis -0.04031220 -0.98362390 0.17566718 Axis point 125.67832095 0.00000000 157.57753081 Rotation angle (degrees) 176.23911220 Shift along axis -0.17945663 > show #!8 models > hide #!9 models > select subtract #10 Nothing selected > hide #!10 models > show #!10 models > hide #!8 models > show #!8 models > hide #!8 models > show #!11 models > hide #!10 models > show #!10 models > select add #11 2 models selected > view matrix models > #11,0.83789,-0.53148,-0.12435,93.216,-0.53452,-0.84509,0.010318,306.1,-0.11057,0.05782,-0.99219,291.46 > view matrix models > #11,0.87567,0.38049,0.29737,-84.014,0.47018,-0.53126,-0.70477,229.85,-0.11018,0.75696,-0.64411,156.03 > view matrix models > #11,0.99273,0.070823,-0.097356,-6.1982,0.016369,-0.88055,-0.47367,302.86,-0.11927,0.46863,-0.87531,225.51 > fitmap #11 inMap #10 Fit map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 45754 points correlation = 0.7386, correlation about mean = -0.02581, overlap = 1355 steps = 168, shift = 17.3, angle = 31.8 degrees Position of cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) relative to cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates: Matrix rotation and translation -0.38917965 0.05095816 -0.91975131 323.90582539 -0.15837916 -0.98730156 0.01231516 285.52055130 -0.90744434 0.15046225 0.39230839 175.68159882 Axis 0.55013716 -0.04900950 -0.83363492 Axis point 230.74773970 125.72052254 0.00000000 Rotation angle (degrees) 172.78707980 Shift along axis 17.74509610 > select subtract #11 Nothing selected > hide #!11 models > hide #!10 models > show #!11 models > hide #!11 models > show #!10 models > hide #!10 models > show #!9 models > hide #!9 models > view P1 > show #!12 models > ui mousemode right translate > save P4_J242_class_4_sharp.png supersample 3 transparentBackground true > hide #!12 models > show #!11 models > save P4_J242_class_3_sharp.png supersample 3 transparentBackground true > hide #!11 models > show #!10 models > save P4_J242_class_2_sharp.png supersample 3 transparentBackground true > hide #!10 models > show #!9 models > view P1 [Repeated 1 time(s)] > save P4_J242_class_1_sharp.png supersample 3 transparentBackground true > hide #!9 models > show #!8 models > save P4_J242_class_0_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow.cxs"" Unsupported scale factor (0.000000) detected on Display1 [Repeated 2 time(s)] > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J117_class_00_00162_volume_sharp.mrc"" Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size 128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32 > hide #!8 models > select add #13 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #13,1,0,0,6.2015,0,1,0,0.69431,0,0,1,-17.516 > ui mousemode right ""rotate selected models"" > view matrix models > #13,-0.13264,-0.68512,-0.71625,337.99,0.0019176,-0.72281,0.69104,120.39,-0.99116,0.090284,0.097186,224.71 > view matrix models > #13,0.0040424,0.12352,-0.99233,257.27,0.14964,-0.98124,-0.12153,245.92,-0.98873,-0.148,-0.02245,270.75 > select subtract #13 Nothing selected > show #!12 models > hide #!12 models > show #!11 models > hide #!11 models > show #!10 models > fitmap #13 inMap #10 Fit map cryosparc_P4_J117_class_00_00162_volume_sharp.mrc in map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 20961 points correlation = 0.8109, correlation about mean = 0.2077, overlap = 1054 steps = 92, shift = 12.7, angle = 18.1 degrees Position of cryosparc_P4_J117_class_00_00162_volume_sharp.mrc (#13) relative to cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates: Matrix rotation and translation -0.98193657 -0.07856914 0.17212633 243.32837219 0.00195692 -0.91387700 -0.40598645 309.66348462 0.18920029 -0.39831610 0.89752300 41.87114917 Axis 0.09277951 -0.20652448 0.97403265 Axis point 116.38449758 161.85402651 0.00000000 Rotation angle (degrees) 177.63092236 Shift along axis -0.59333628 > hide #!10 models > hide #!13 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J117_class_01_00162_volume_sharp.mrc"" Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size 128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32 > select add #14 2 models selected > view matrix models > #14,-0.39254,-0.77748,0.49135,234.79,-0.04345,-0.51796,-0.8543,320.26,0.91871,-0.3567,0.16954,27.288 > view matrix models > #14,-0.061348,0.89979,0.432,-25.376,-0.288,-0.43036,0.85548,115.2,0.95566,-0.071931,0.28554,-30.976 > view matrix models > #14,-0.046716,0.65995,-0.74985,161.94,-0.070464,0.74662,0.6615,-44.914,0.99642,0.08374,0.011624,-20.712 > select subtract #14 Nothing selected > show #!13 models > fitmap #14 inMap #13 Fit map cryosparc_P4_J117_class_01_00162_volume_sharp.mrc in map cryosparc_P4_J117_class_00_00162_volume_sharp.mrc using 20968 points correlation = 0.846, correlation about mean = 0.3465, overlap = 1110 steps = 132, shift = 18.5, angle = 19.5 degrees Position of cryosparc_P4_J117_class_01_00162_volume_sharp.mrc (#14) relative to cryosparc_P4_J117_class_00_00162_volume_sharp.mrc (#13) coordinates: Matrix rotation and translation -0.99955515 0.02982234 0.00035424 260.68209471 -0.00628473 -0.19900464 -0.97997839 284.54003350 -0.02915475 -0.97954468 0.19910354 244.04930876 Axis 0.00930049 0.63278447 -0.77427212 Axis point 133.98017190 240.03303746 0.00000000 Rotation angle (degrees) 178.66392593 Shift along axis -6.48359029 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J117_class_02_00162_volume_sharp.mrc"" Opened cryosparc_P4_J117_class_02_00162_volume_sharp.mrc as #15, grid size 128,128,128, pixel 2.08, shown at level 0.251, step 1, values float32 > hide #!13 models > select add #14 2 models selected > show #!12 models > select subtract #14 Nothing selected > hide #!14 models > select add #15 2 models selected > view matrix models > #15,-0.98221,0.18526,0.030552,219.51,0.18651,0.98144,0.044675,-26.394,-0.021708,0.049578,-0.99853,243.73 > ui mousemode right ""translate selected models"" > view matrix models > #15,-0.98221,0.18526,0.030552,234.62,0.18651,0.98144,0.044675,-36.86,-0.021708,0.049578,-0.99853,271.78 > fitmap #15 inMap #12 Fit map cryosparc_P4_J117_class_02_00162_volume_sharp.mrc in map cryosparc_P4_J242_class_04_00122_volume_sharp.mrc using 20967 points correlation = 0.781, correlation about mean = 0.07908, overlap = 1573 steps = 76, shift = 10.9, angle = 6.65 degrees Position of cryosparc_P4_J117_class_02_00162_volume_sharp.mrc (#15) relative to cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.82536305 0.56130744 0.06090799 -57.36751075 -0.56057744 0.82755504 -0.03009290 101.38226037 -0.06729608 -0.00930608 0.99768964 1.14989876 Axis 0.01840555 0.11351744 -0.99336550 Axis point 134.55599767 144.37243816 0.00000000 Rotation angle (degrees) 34.38068857 Shift along axis 9.31050435 > volume flip #15 Opened cryosparc_P4_J117_class_02_00162_volume_sharp.mrc z flip as #16, grid size 128,128,128, pixel 2.08, shown at step 1, values float32 > close #15 > select add #16 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #16,-0.81511,-0.57721,0.04929,312.41,0.52972,-0.77708,-0.33992,218.14,0.2345,-0.25096,0.93916,8.6526 > fitmap #15 inMap #12 No atoms or maps for #15 > fitmap #16 inMap #12 Fit map cryosparc_P4_J117_class_02_00162_volume_sharp.mrc z flip in map cryosparc_P4_J242_class_04_00122_volume_sharp.mrc using 20967 points correlation = 0.9777, correlation about mean = 0.7437, overlap = 2747 steps = 108, shift = 14.1, angle = 17.5 degrees Position of cryosparc_P4_J117_class_02_00162_volume_sharp.mrc z flip (#16) relative to cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.94024990 -0.32652551 -0.09649458 65.60674301 -0.33221344 -0.94188358 -0.04989541 307.74881291 -0.07459454 0.07897095 -0.99408211 253.25354142 Axis 0.98493295 -0.16738329 -0.04347315 Axis point 0.00000000 155.23786381 133.19610246 Rotation angle (degrees) 176.24909728 Shift along axis 2.09650544 > select subtract #16 Nothing selected > rename #16 CS_P4_J117_class_02_sharp_flip.mrc id #15 > save CS_P4_J117_class_02_sharp_flip.mrc #15 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J117_class_03_00162_volume_sharp.mrc"" Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size 128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32 > hide #!12 models > hide #!15 models > select add #16 2 models selected > show #!14 models > view matrix models > #16,0.00021536,0.34795,0.93751,-37.63,0.50671,0.80821,-0.30007,0.053261,-0.86212,0.47511,-0.17613,183.13 > hide #!14 models > view matrix models > #16,0.63015,0.10301,-0.76961,125.95,-0.74582,0.35606,-0.56301,261.02,0.21603,0.92877,0.3012,-81.743 > view matrix models > #16,0.63277,-0.43368,-0.64151,190.37,0.75188,0.14602,0.64293,-47.242,-0.18515,-0.88916,0.41847,227.83 > show #!13 models > hide #!13 models > show #!12 models > hide #!12 models > show #!11 models > ui mousemode right ""translate selected models"" > view matrix models > #16,0.63277,-0.43368,-0.64151,206.09,0.75188,0.14602,0.64293,-70.694,-0.18515,-0.88916,0.41847,249.05 > view matrix models > #16,0.63277,-0.43368,-0.64151,204.5,0.75188,0.14602,0.64293,-75.196,-0.18515,-0.88916,0.41847,240.94 > ui mousemode right ""rotate selected models"" > view matrix models > #16,-0.30976,-0.38252,-0.87047,346.06,0.94397,-0.2334,-0.23335,63.654,-0.1139,-0.89398,0.43339,230.67 > fitmap #16 inMap #11 Fit map cryosparc_P4_J117_class_03_00162_volume_sharp.mrc in map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc using 20958 points correlation = 0.9023, correlation about mean = 0.3197, overlap = 1117 steps = 184, shift = 6.54, angle = 53.8 degrees Position of cryosparc_P4_J117_class_03_00162_volume_sharp.mrc (#16) relative to cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) coordinates: Matrix rotation and translation 0.41743274 -0.19488532 -0.88756388 222.32976103 -0.90862481 -0.10271919 -0.40478358 322.57606660 -0.01228347 0.97543246 -0.21995599 21.59894000 Axis 0.77392148 -0.49079151 -0.40021149 Axis point 0.00000000 222.40854643 197.20887777 Rotation angle (degrees) 116.91198346 Shift along axis 5.10403978 > select subtract #16 Nothing selected > hide #!11 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J117_class_04_00162_volume_sharp.mrc"" Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 > hide #!16 models > select add #17 2 models selected > show #!13 models > hide #!13 models > show #!11 models > hide #!11 models > show #!10 models > hide #!17 models > show #!17 models > view matrix models > #17,-0.0034658,-0.079884,-0.9968,294.42,-0.15421,0.98492,-0.078396,35.543,0.98803,0.15344,-0.015732,-30.795 > fitmap #17 inMap #10 Fit map cryosparc_P4_J117_class_04_00162_volume_sharp.mrc in map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 20958 points correlation = 0.8416, correlation about mean = 0.3036, overlap = 1170 steps = 148, shift = 13.9, angle = 32.2 degrees Position of cryosparc_P4_J117_class_04_00162_volume_sharp.mrc (#17) relative to cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates: Matrix rotation and translation 0.73519379 0.67627298 0.04631360 -60.93633283 -0.67522557 0.73664284 -0.03778583 134.15115598 -0.05967011 -0.00349222 0.99821205 3.94076312 Axis 0.02528875 0.07815439 -0.99662047 Axis point 141.29888305 145.62167557 0.00000000 Rotation angle (degrees) 42.69072745 Shift along axis 5.01605257 > select subtract #17 Nothing selected > hide #!10 models > show #!10 models > hide #!17 models > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow.cxs"" > show #!13 models > hide #!10 models > color #13 #FCEDFF > hide #!13 models > show #!14 models > color #14 #FCEDFF > show #!15 models > hide #!14 models > hide #!15 models > show #!16 models > color #16 #FCEDFF > hide #!16 models > show #!17 models > color #17 #FCEDFF > show #!15 models > hide #!17 models > color #15 #99BFE5 > volume #15 level 0.3349 > ui mousemode right translate > view P1 [Repeated 1 time(s)] > save P4_J117_class_2_sharp.png supersample 3 transparentBackground true > hide #!15 models > show #!13 models > save P4_J117_class_0_sharp.png supersample 3 transparentBackground true > hide #!13 models > show #!14 models > save P4_J117_class_1_sharp.png supersample 3 transparentBackground true > hide #!14 models > show #!16 models > save P4_J117_class_3_sharp.png supersample 3 transparentBackground true > hide #!16 models > show #!17 models > save P4_J117_class_4_sharp.png supersample 3 transparentBackground true [Repeated 1 time(s)] > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J120_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J120_002_volume_map_sharp.mrc as #18, grid size 80,80,80, pixel 3.32, shown at level 1.08, step 1, values float32 > hide #!17 models > show #!15 models > select add #18 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #18,0.9199,0.35329,0.17023,-57.439,0.37414,-0.92071,-0.11099,219.04,0.11752,0.16579,-0.97913,208.75 > ui mousemode right ""translate selected models"" > view matrix models > #18,0.9199,0.35329,0.17023,-56.147,0.37414,-0.92071,-0.11099,218.08,0.11752,0.16579,-0.97913,234.23 > ui mousemode right ""rotate selected models"" > view matrix models > #18,0.47537,0.87487,0.092902,-59.652,0.86989,-0.48319,0.099115,73.008,0.1316,0.033698,-0.99073,251.23 > volume flip #18 Opened cryosparc_P4_J120_002_volume_map_sharp.mrc z flip as #19, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > select subtract #18 Nothing selected > close #18 > select add #19 2 models selected > view matrix models > #19,0.011836,0.9987,-0.049536,1.5471,-0.96239,0.024824,0.27053,210.58,0.27141,0.044471,0.96144,-38.44 > ui mousemode right ""translate selected models"" > view matrix models > #19,0.011836,0.9987,-0.049536,5.1894,-0.96239,0.024824,0.27053,209.75,0.27141,0.044471,0.96144,-23.291 > fitmap #19 inMap #15 Fit map cryosparc_P4_J120_002_volume_map_sharp.mrc z flip in map CS_P4_J117_class_02_sharp_flip.mrc using 5118 points correlation = 0.9182, correlation about mean = 0.533, overlap = 3573 steps = 76, shift = 9.96, angle = 10.7 degrees Position of cryosparc_P4_J120_002_volume_map_sharp.mrc z flip (#19) relative to CS_P4_J117_class_02_sharp_flip.mrc (#15) coordinates: Matrix rotation and translation -0.48058823 -0.86458262 0.14673736 288.72558748 0.85464108 -0.49926017 -0.14257599 104.76974006 0.19652884 0.05688743 0.97884638 -28.97188121 Axis 0.11519876 -0.02875674 0.99292613 Axis point 115.59153027 135.80137987 0.00000000 Rotation angle (degrees) 120.03315219 Shift along axis 1.48105620 > ui mousemode right ""rotate selected models"" > view matrix models > #19,0.89305,-0.32489,-0.3113,106.99,0.34183,0.93976,-0.00013805,-25.175,0.29259,-0.10629,0.95031,-3.3753 > ui mousemode right ""translate selected models"" > view matrix models > #19,0.89305,-0.32489,-0.3113,96.178,0.34183,0.93976,-0.00013805,-42.263,0.29259,-0.10629,0.95031,-5.1551 > fitmap #19 inMap #15 Fit map cryosparc_P4_J120_002_volume_map_sharp.mrc z flip in map CS_P4_J117_class_02_sharp_flip.mrc using 5118 points correlation = 0.9187, correlation about mean = 0.5356, overlap = 3578 steps = 76, shift = 8.31, angle = 8.52 degrees Position of cryosparc_P4_J120_002_volume_map_sharp.mrc z flip (#19) relative to CS_P4_J117_class_02_sharp_flip.mrc (#15) coordinates: Matrix rotation and translation -0.47913034 0.85546358 0.19651003 54.96243137 -0.86530880 -0.49790427 0.05772364 303.37608678 0.14722365 -0.14238471 0.97880120 3.73022055 Axis -0.11546470 0.02843878 -0.99290440 Axis point 115.58296139 135.79077530 0.00000000 Rotation angle (degrees) 119.94157891 Shift along axis -1.42232844 > hide #!19 models > hide #!15 models > show #!15 models > hide #!15 models > show #!19 models > select subtract #19 Nothing selected > show #!15 models > hide #!15 models > rename #19 CS_P4_J120_sharp_flip id #18 > save CS_P4_J120_sharp_flip.mrc #18 > volume #18 level 1.185 > volume #18 level 1.639 > volume #18 step 2 > volume #18 step 1 > show #!15 models > volume #18 level 1.559 > hide #!15 models > volume #18 level 1.292 > view P1 > color #18 #99BFE5 > show #!17 models > hide #!17 models > hide #!18 models > show #!18 models > save P4_J120_NU_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J169_class_00_00182_volume_sharp.mrc"" Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size 128,128,128, pixel 2.08, shown at level 0.175, step 1, values float32 > select add #19 2 models selected > hide #!18 models > show #!18 models > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models #19,1,0,0,-7.1681,0,1,0,-1.6755,0,0,1,29.407 > fitmap #19 inMap #18 Fit map cryosparc_P4_J169_class_00_00182_volume_sharp.mrc in map CS_P4_J120_sharp_flip.mrc using 20970 points correlation = 0.3797, correlation about mean = 0.05313, overlap = 2374 steps = 192, shift = 6.4, angle = 17.5 degrees Position of cryosparc_P4_J169_class_00_00182_volume_sharp.mrc (#19) relative to CS_P4_J120_sharp_flip.mrc (#18) coordinates: Matrix rotation and translation 0.64594502 0.66965380 0.36649532 -93.21942227 -0.65111130 0.73392063 -0.19342850 149.32350272 -0.39850860 -0.11368507 0.91009153 102.27587247 Axis 0.05217441 0.50052557 -0.86414813 Axis point 153.99219258 219.18137479 0.00000000 Rotation angle (degrees) 49.83592965 Shift along axis -18.50494005 > select subtract #19 Nothing selected > hide #!18 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J169_class_01_00182_volume_sharp.mrc"" Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size 128,128,128, pixel 2.08, shown at level 0.189, step 1, values float32 > hide #!19 models > show #!17 models > select add #20 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #20,0.023382,0.1088,0.99379,-27.517,0.050205,0.99268,-0.10986,9.6432,-0.99847,0.052462,0.017749,251.64 > hide #!17 models > show #!16 models > hide #!16 models > show #!15 models > hide #!15 models > show #!14 models > ui mousemode right ""translate selected models"" > view matrix models > #20,0.023382,0.1088,0.99379,-22.964,0.050205,0.99268,-0.10986,7.1023,-0.99847,0.052462,0.017749,242.74 > ui mousemode right ""rotate selected models"" > view matrix models > #20,-0.029978,-0.71994,-0.69339,335.92,-0.21064,-0.67357,0.70847,177,-0.9771,0.16729,-0.13145,243.19 > ui mousemode right ""translate selected models"" > view matrix models > #20,-0.029978,-0.71994,-0.69339,328.25,-0.21064,-0.67357,0.70847,170.9,-0.9771,0.16729,-0.13145,240.41 > fitmap #20 inMap #14 Fit map cryosparc_P4_J169_class_01_00182_volume_sharp.mrc in map cryosparc_P4_J117_class_01_00162_volume_sharp.mrc using 20954 points correlation = 0.8829, correlation about mean = 0.4124, overlap = 1200 steps = 104, shift = 14, angle = 14 degrees Position of cryosparc_P4_J169_class_01_00182_volume_sharp.mrc (#20) relative to cryosparc_P4_J117_class_01_00162_volume_sharp.mrc (#14) coordinates: Matrix rotation and translation -0.94773816 0.28655181 -0.14028702 243.79600144 -0.24891252 -0.93914826 -0.23673424 326.23627964 -0.19958693 -0.18944287 0.96139298 60.20896934 Axis 0.08744550 0.10965027 -0.99011621 Axis point 147.27291182 149.47535150 0.00000000 Rotation angle (degrees) 164.31164420 Shift along axis -2.52311906 > select subtract #20 Nothing selected > hide #!14 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J169_class_02_00182_volume_sharp.mrc"" Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size 128,128,128, pixel 2.08, shown at level 0.216, step 1, values float32 > hide #!20 models > select add #21 2 models selected > view matrix models #21,1,0,0,-13.073,0,1,0,8.3491,0,0,1,8.6967 > ui mousemode right ""rotate selected models"" > view matrix models > #21,-0.06365,0.67952,0.73089,-53.58,-0.2928,0.68743,-0.66461,177.89,-0.95405,-0.25631,0.15521,285.48 > view matrix models > #21,0.10048,-0.44353,0.89061,41.096,0.13793,-0.88029,-0.45395,284.46,0.98533,0.16846,-0.027275,-4.3073 > fitmap #21 inMap #20 Fit map cryosparc_P4_J169_class_02_00182_volume_sharp.mrc in map cryosparc_P4_J169_class_01_00182_volume_sharp.mrc using 20962 points correlation = 0.7829, correlation about mean = 0.1539, overlap = 900.6 steps = 188, shift = 21.5, angle = 32 degrees Position of cryosparc_P4_J169_class_02_00182_volume_sharp.mrc (#21) relative to cryosparc_P4_J169_class_01_00182_volume_sharp.mrc (#20) coordinates: Matrix rotation and translation -0.75680258 0.56772680 0.32393846 109.96194933 0.37589927 0.78345603 -0.49487007 56.85693302 -0.53474254 -0.25275071 -0.80632963 338.09031391 Axis 0.26532092 0.94096581 -0.21020979 Axis point 90.65236627 0.00000000 161.68382083 Rotation angle (degrees) 152.85290905 Shift along axis 11.60574300 > show #!20 models > select subtract #21 Nothing selected > select add #21 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #21,0.31625,-0.43913,0.84092,24.723,-0.35094,-0.87769,-0.32634,336.73,0.88138,-0.19191,-0.43168,94.219 > ui mousemode right ""rotate selected models"" > view matrix models > #21,0.23561,0.79493,-0.55908,75.399,0.21977,0.51679,0.82742,-71.321,0.94667,-0.31782,-0.052938,48.925 > ui mousemode right ""translate selected models"" > view matrix models > #21,0.23561,0.79493,-0.55908,69.861,0.21977,0.51679,0.82742,-70.077,0.94667,-0.31782,-0.052938,40.098 > fitmap #21 inMap #20 Fit map cryosparc_P4_J169_class_02_00182_volume_sharp.mrc in map cryosparc_P4_J169_class_01_00182_volume_sharp.mrc using 20962 points correlation = 0.8883, correlation about mean = 0.4082, overlap = 1398 steps = 80, shift = 8.95, angle = 4.79 degrees Position of cryosparc_P4_J169_class_02_00182_volume_sharp.mrc (#21) relative to cryosparc_P4_J169_class_01_00182_volume_sharp.mrc (#20) coordinates: Matrix rotation and translation -0.99875153 -0.02706229 -0.04198798 281.31180443 0.03395891 -0.98426911 -0.17338138 286.61926959 -0.03663538 -0.17459079 0.98395929 28.58358251 Axis -0.01973976 -0.08736459 0.99598081 Axis point 138.73615561 146.72655614 0.00000000 Rotation angle (degrees) 178.24454217 Shift along axis -2.12470384 > select subtract #21 Nothing selected > hide #!20 models > hide #!21 models > show #!21 models > show #!20 models > hide #!21 models > show #!21 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J169_class_03_00182_volume_sharp.mrc"" Opened cryosparc_P4_J169_class_03_00182_volume_sharp.mrc as #22, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 > hide #!20 models > hide #!21 models > select add #22 2 models selected > show #!18 models > ui mousemode right ""rotate selected models"" > view matrix models > #22,0.80286,-0.54835,0.23395,74.113,-0.54307,-0.83458,-0.092472,336.96,0.24595,-0.052807,-0.96784,209.56 > view matrix models > #22,0.23802,0.97115,0.01476,-30.605,0.97056,-0.2384,0.03436,32.801,0.036887,0.0061467,-0.9993,233.87 > ui mousemode right ""translate selected models"" > view matrix models > #22,0.23802,0.97115,0.01476,-35.135,0.97056,-0.2384,0.03436,31.843,0.036887,0.0061467,-0.9993,265.72 > view matrix models > #22,0.23802,0.97115,0.01476,-30.091,0.97056,-0.2384,0.03436,32.303,0.036887,0.0061467,-0.9993,265.71 > select subtract #22 Nothing selected > hide #!18 models > volume flip #22 Opened cryosparc_P4_J169_class_03_00182_volume_sharp.mrc z flip as #23, grid size 128,128,128, pixel 2.08, shown at step 1, values float32 > close #22 > show #!21 models > hide #!21 models > show #!18 models > select add #23 2 models selected > view matrix models > #23,0.23802,0.97115,0.01476,-34.192,0.97056,-0.2384,0.03436,27.412,0.036887,0.0061467,-0.9993,278.73 > ui mousemode right ""rotate selected models"" > view matrix models > #23,-0.23315,-0.92003,-0.31494,337.04,0.93397,-0.30205,0.19095,18.61,-0.27081,-0.24962,0.92971,78.293 > ui mousemode right ""translate selected models"" > view matrix models > #23,-0.23315,-0.92003,-0.31494,335.86,0.93397,-0.30205,0.19095,18.866,-0.27081,-0.24962,0.92971,88.616 > fitmap #23 inMap #18 Fit map cryosparc_P4_J169_class_03_00182_volume_sharp.mrc z flip in map CS_P4_J120_sharp_flip.mrc using 20952 points correlation = 0.9077, correlation about mean = 0.6695, overlap = 1.202e+04 steps = 60, shift = 4.34, angle = 10.2 degrees Position of cryosparc_P4_J169_class_03_00182_volume_sharp.mrc z flip (#23) relative to CS_P4_J120_sharp_flip.mrc (#18) coordinates: Matrix rotation and translation 0.17479617 -0.97573598 0.13185442 219.49728105 0.98179238 0.18284123 0.05150543 -32.00811477 -0.07436413 0.12045072 0.98993010 -9.54926019 Axis 0.03500529 0.10470244 0.99388733 Axis point 128.78581299 116.22335978 0.00000000 Rotation angle (degrees) 79.99211268 Shift along axis -5.15865059 > select subtract #23 Nothing selected > hide #!18 models > rename #23 CS_P4_J169_class_03_sharp_flip id #22 > save CS_P4_J169_class_03_sharp_flip.mrc #22 > show #!21 models > hide #!21 models > show #!18 models > hide #!18 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J169_class_04_00182_volume_sharp.mrc"" Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size 128,128,128, pixel 2.08, shown at level 0.171, step 1, values float32 > hide #!22 models > show #!21 models > select add #23 2 models selected > view matrix models #23,1,0,0,62.54,0,1,0,-0.93224,0,0,1,-9.0713 > ui mousemode right ""rotate selected models"" > view matrix models > #23,0.11131,-0.99321,-0.033862,304.62,-0.95598,-0.11633,0.2694,223.09,-0.27151,0.0023841,-0.96243,297.1 > view matrix models > #23,0.14785,0.8725,0.4657,-3.2346,-0.24604,0.48852,-0.83714,210.48,-0.95792,0.0091875,0.2869,210.23 > ui mousemode right ""translate selected models"" > view matrix models > #23,0.14785,0.8725,0.4657,-72.613,-0.24604,0.48852,-0.83714,211.81,-0.95792,0.0091875,0.2869,205.44 > ui mousemode right ""rotate selected models"" > view matrix models > #23,-0.12372,0.72067,0.68215,-49.094,0.065146,0.69184,-0.7191,130.45,-0.99018,-0.044529,-0.13254,274.4 > ui mousemode right ""translate selected models"" > view matrix models > #23,-0.12372,0.72067,0.68215,-52.059,0.065146,0.69184,-0.7191,130.58,-0.99018,-0.044529,-0.13254,270.2 > fitmap #23 inMap #21 Fit map cryosparc_P4_J169_class_04_00182_volume_sharp.mrc in map cryosparc_P4_J169_class_02_00182_volume_sharp.mrc using 20956 points correlation = 0.8996, correlation about mean = 0.4033, overlap = 1373 steps = 168, shift = 14.7, angle = 39.5 degrees Position of cryosparc_P4_J169_class_04_00182_volume_sharp.mrc (#23) relative to cryosparc_P4_J169_class_02_00182_volume_sharp.mrc (#21) coordinates: Matrix rotation and translation -0.99961182 0.01552465 -0.02313457 267.26750037 0.02397017 0.90245504 -0.43011668 70.06567251 0.01420050 -0.43050425 -0.90247684 305.57661651 Axis -0.01012464 -0.97530665 0.22062281 Axis point 131.76679627 0.00000000 162.02424501 Rotation angle (degrees) 178.90328205 Shift along axis -3.62433410 > select subtract #23 Nothing selected > hide #!23 models > hide #!21 models > show #!23 models > volume #23 level 0.1996 > hide #!23 models > show #!22 models > volume #22 level 0.2715 > hide #!22 models > show #!21 models > volume #21 level 0.2481 > hide #!21 models > show #!20 models > volume #20 level 0.198 > hide #!20 models > show #!19 models > volume #19 level 0.1357 > volume #19 level 0.1565 > color #9 #FCEDFF > show #!9 models > hide #!9 models > color #19 #FCEDFF > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow.cxs"" > hide #!19 models > show #!20 models > color #20 #FCEDFF > hide #!20 models > show #!21 models > show #!20 models > hide #!20 models > color #21 #FCEDFF > hide #!21 models > show #!22 models > show #!23 models > hide #!22 models > color #23 #FCEDFF > color #22 #99BFE5 > show #!22 models > hide #!23 models > hide #!22 models > show #!22 models > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow.cxs"" > view P1 > save P4_J169_class_3_sharp.png supersample 3 transparentBackground true > hide #!22 models > show #!19 models > save P4_J169_class_0_sharp.png supersample 3 transparentBackground true > hide #!19 models > show #!20 models > save P4_J169_class_1_sharp.png supersample 3 transparentBackground true > hide #!20 models > show #!21 models > save P4_J169_class_2_sharp.png supersample 3 transparentBackground true > hide #!21 models > show #!22 models > show #!23 models > hide #!22 models > save P4_J169_class_4_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J176_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J176_002_volume_map_sharp.mrc as #24, grid size 80,80,80, pixel 3.32, shown at level 1.05, step 1, values float32 > show #!22 models > hide #!23 models > select add #24 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #24,0.60544,-0.7944,-0.048687,168.77,-0.79404,-0.60707,0.031193,325.29,-0.054337,0.019774,-0.99833,244.32 > view matrix models > #24,0.59955,-0.80023,-0.012763,166.07,-0.79939,-0.59954,0.03913,324.05,-0.038965,-0.013258,-0.99915,246.8 > view matrix models > #24,0.55506,-0.74882,-0.36218,207.08,-0.8209,-0.56341,-0.093219,337.96,-0.13425,0.34906,-0.92744,201.93 > view matrix models > #24,0.18767,0.98161,-0.034938,-17.516,0.95411,-0.19063,-0.23093,58.314,-0.23335,0.010004,-0.97234,267.28 > volume flip #24 Opened cryosparc_P4_J176_002_volume_map_sharp.mrc z flip as #25, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #24 > select add #25 2 models selected > view matrix models > #25,-0.63444,0.77032,-0.064025,129.07,-0.77136,-0.63629,-0.011971,326.31,-0.04996,0.041792,0.99788,-43.633 > ui mousemode right ""translate selected models"" > view matrix models > #25,-0.63444,0.77032,-0.064025,133.77,-0.77136,-0.63629,-0.011971,326.45,-0.04996,0.041792,0.99788,5.2846 > fitmap #25 inMap #22 Fit map cryosparc_P4_J176_002_volume_map_sharp.mrc z flip in map CS_P4_J169_class_03_sharp_flip.mrc using 5115 points correlation = 0.927, correlation about mean = 0.5943, overlap = 3935 steps = 92, shift = 11.4, angle = 9.34 degrees Position of cryosparc_P4_J176_002_volume_map_sharp.mrc z flip (#25) relative to CS_P4_J169_class_03_sharp_flip.mrc (#22) coordinates: Matrix rotation and translation -0.48979714 -0.86290735 -0.12445753 333.02911722 0.86312907 -0.50006428 0.07031310 74.16708713 -0.12291046 -0.07298376 0.98973047 29.10111268 Axis -0.08273609 -0.00089324 0.99657109 Axis point 146.24021491 133.58927656 0.00000000 Rotation angle (degrees) 120.00433179 Shift along axis 1.38155071 > select subtract #25 Nothing selected > rename #25 CS_P4_J176_NU_sharp_flip id #24 > save CS_P4_J176_NU_sharp_flip.mrc #24 > hide #!22 models > volume #24 level 1.757 > volume #24 level 1.364 > color #24 #99BFE5 > volume #24 level 1.6 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow.cxs"" > view P1 > save CS_P4_J176_NU_sharp.png supersample 3 transparentBackground true > open ""/Users/peiyuyu/Documents/Goethe University/19. Model Building/2. AcrF > Project/1. Apo-form/LG-F_Apo/Map/cryosparc_P10_J41_007_volume_map_sharp.mrc"" Opened cryosparc_P10_J41_007_volume_map_sharp.mrc as #25, grid size 320,320,320, pixel 0.831, shown at level 0.123, step 2, values float32 > hide #!24 models > show #!22 models > hide #!22 models > volume #25 level 0.2164 > save CS_P10_J41_NU_sharp_flip.mrc #25 > close #25 > show #!24 models > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow1.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J255_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J255_002_volume_map_sharp.mrc as #25, grid size 80,80,80, pixel 3.32, shown at level 0.649, step 1, values float32 > hide #!24 models > volume flip #25 Opened cryosparc_P4_J255_002_volume_map_sharp.mrc z flip as #26, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #25 > rename CS_P4_J255_sharp_flip id #25 Missing or invalid ""models"" argument: invalid models specifier > rename #26 CS_P4_J255_sharp_flip id #25 > save CS_P4_J255_sharp_flip.mrc #25 > show #!21 models > hide #!21 models > show #!24 models > fitmap #25 inMap #24 Fit map CS_P4_J255_sharp_flip.mrc in map CS_P4_J176_NU_sharp_flip.mrc using 5116 points correlation = 0.3392, correlation about mean = 0.06206, overlap = 2168 steps = 64, shift = 8.32, angle = 5.45 degrees Position of CS_P4_J255_sharp_flip.mrc (#25) relative to CS_P4_J176_NU_sharp_flip.mrc (#24) coordinates: Matrix rotation and translation -0.61720035 -0.75989860 -0.20400451 353.05950420 0.73150715 -0.64968488 0.20689815 96.93395715 -0.28976026 -0.02153315 0.95685700 43.12583281 Axis -0.15115555 0.05674554 0.98687990 Axis point 157.34041998 128.70985965 0.00000000 Rotation angle (degrees) 130.92072050 Shift along axis -5.30631665 > ui mousemode right ""rotate selected models"" > select add #25 2 models selected > view matrix models > #25,-0.47042,-0.83357,-0.28961,363.38,0.84754,-0.51818,0.11478,76.044,-0.24575,-0.19146,0.95024,72.926 > ui mousemode right ""translate selected models"" > view matrix models > #25,-0.47042,-0.83357,-0.28961,355.09,0.84754,-0.51818,0.11478,66.81,-0.24575,-0.19146,0.95024,74.95 > view matrix models > #25,-0.47042,-0.83357,-0.28961,355.15,0.84754,-0.51818,0.11478,66.803,-0.24575,-0.19146,0.95024,74.561 > fitmap #25 inMap #24 Fit map CS_P4_J255_sharp_flip.mrc in map CS_P4_J176_NU_sharp_flip.mrc using 5116 points correlation = 0.8943, correlation about mean = 0.6059, overlap = 8709 steps = 84, shift = 8.95, angle = 14.5 degrees Position of CS_P4_J255_sharp_flip.mrc (#25) relative to CS_P4_J176_NU_sharp_flip.mrc (#24) coordinates: Matrix rotation and translation -0.48869161 0.86324945 -0.12641554 102.63693670 -0.86157381 -0.50031742 -0.08586638 328.42188396 -0.13737200 0.06695414 0.98825405 11.50507804 Axis 0.08825319 0.00632731 -0.99607798 Axis point 146.96136624 134.50878130 0.00000000 Rotation angle (degrees) 120.02497766 Shift along axis -0.32389146 > select subtract #25 Nothing selected > save CS_P4_J255_sharp_flip.mrc #25 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J256_003_volume_map_sharp.mrc"" Opened cryosparc_P4_J256_003_volume_map_sharp.mrc as #26, grid size 80,80,80, pixel 3.32, shown at level 1.01, step 1, values float32 > hide #!25 models > hide #!24 models > select add #26 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #26,-0.89385,-0.39986,0.20284,290.33,-0.34063,0.89978,0.2727,28.49,-0.29155,0.17466,-0.94047,242.77 > select subtract #26 Nothing selected > show #!25 models > fitmap #26 inMap #25 Fit map cryosparc_P4_J256_003_volume_map_sharp.mrc in map CS_P4_J255_sharp_flip.mrc using 5120 points correlation = 0.5232, correlation about mean = 0.0553, overlap = 3214 steps = 120, shift = 25.3, angle = 15.3 degrees Position of cryosparc_P4_J256_003_volume_map_sharp.mrc (#26) relative to CS_P4_J255_sharp_flip.mrc (#25) coordinates: Matrix rotation and translation -0.15531756 0.84438274 0.51273214 -19.64184672 0.98713928 0.15254692 0.04780678 -29.86548711 -0.03784849 0.51356326 -0.85721658 167.46829582 Axis 0.63355180 0.74893504 0.19418658 Axis point 24.16142457 0.00000000 89.91884511 Rotation angle (degrees) 158.43381860 Shift along axis -2.29134077 > select add #26 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #26,-0.87857,-0.47692,-0.025855,314.85,-0.44818,0.80449,0.38978,38.161,-0.16509,0.35404,-0.92054,233.61 > ui mousemode right ""rotate selected models"" > view matrix models > #26,-0.93629,-0.25688,0.23952,260.92,-0.23661,0.96532,0.11035,19.606,-0.25956,0.046645,-0.9646,294.56 > ui mousemode right ""translate selected models"" > view matrix models > #26,-0.93629,-0.25688,0.23952,186.31,-0.23661,0.96532,0.11035,26.555,-0.25956,0.046645,-0.9646,285.53 > select subtract #26 Nothing selected > volume flip #26 Opened cryosparc_P4_J256_003_volume_map_sharp.mrc z flip as #27, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #26 > select add #27 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #27,-0.91261,-0.40844,0.017647,236.5,0.22697,-0.47029,0.85283,55.691,-0.34003,0.78231,0.5219,-22.328 > view matrix models > #27,-0.9144,-0.40478,0.0045882,238.13,0.22235,-0.49276,0.84128,61.136,-0.33827,0.77029,0.54058,-23.608 > view matrix models > #27,-0.50015,0.79795,-0.33634,63.369,-0.80597,-0.57099,-0.15615,357.35,-0.31664,0.19298,0.92871,-2.4372 > ui mousemode right ""translate selected models"" > view matrix models > #27,-0.50015,0.79795,-0.33634,139.66,-0.80597,-0.57099,-0.15615,346.55,-0.31664,0.19298,0.92871,33.757 > fitmap #27 inMap #25 Fit map cryosparc_P4_J256_003_volume_map_sharp.mrc z flip in map CS_P4_J255_sharp_flip.mrc using 5120 points correlation = 0.5523, correlation about mean = 0.08213, overlap = 3668 steps = 72, shift = 2.85, angle = 5.49 degrees Position of cryosparc_P4_J256_003_volume_map_sharp.mrc z flip (#27) relative to CS_P4_J255_sharp_flip.mrc (#25) coordinates: Matrix rotation and translation -0.50078193 -0.83716343 -0.21994286 353.70374510 0.81104417 -0.54259583 0.21862553 68.19134780 -0.30236538 -0.06889966 0.95069870 54.62167416 Axis -0.17164375 0.04920372 0.98392958 Axis point 162.79794553 129.91438640 0.00000000 Rotation angle (degrees) 123.11624986 Shift along axis -3.61188964 > view matrix models > #27,-0.56613,0.75777,-0.32448,155.66,-0.74832,-0.63753,-0.18323,351.66,-0.34571,0.13908,0.92798,47.028 > ui mousemode right ""rotate selected models"" > view matrix models > #27,0.96274,0.27031,-0.0085132,-30.789,-0.27044,0.96237,-0.026732,40.459,0.00096683,0.028039,0.99961,4.8234 > fitmap #27 inMap #25 Fit map cryosparc_P4_J256_003_volume_map_sharp.mrc z flip in map CS_P4_J255_sharp_flip.mrc using 5120 points correlation = 0.9111, correlation about mean = 0.5876, overlap = 9195 steps = 60, shift = 4.49, angle = 4.9 degrees Position of cryosparc_P4_J256_003_volume_map_sharp.mrc z flip (#27) relative to CS_P4_J255_sharp_flip.mrc (#25) coordinates: Matrix rotation and translation -0.48877401 0.86149397 -0.13757950 104.57166396 -0.86119668 -0.50165763 -0.08173068 327.97179743 -0.13942829 0.07853517 0.98711295 10.19538079 Axis 0.09263223 0.00106859 -0.99569982 Axis point 147.63593381 133.73777093 0.00000000 Rotation angle (degrees) 120.10984192 Shift along axis -0.11436514 > select subtract #27 Nothing selected > hide #!25 models > rename #27 CS_P4_J256_sharp_flip id #26 > save CS_P4_J256_sharp_flip.mrc #26 > show #!25 models > hide #!25 models > hide #!26 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J257_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J257_002_volume_map_sharp.mrc as #27, grid size 80,80,80, pixel 3.32, shown at level 0.915, step 1, values float32 > select add #27 2 models selected > show #!26 models > view matrix models > #27,0.43348,0.88304,0.17982,-64.533,0.89699,-0.44198,0.0081618,72.887,0.086685,0.15776,-0.98367,205.49 > hide #!26 models > select subtract #27 Nothing selected > volume flip #27 Opened cryosparc_P4_J257_002_volume_map_sharp.mrc z flip as #28, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #27 > select add #28 2 models selected > show #!26 models > view matrix models > #28,0.0384,0.0015757,0.99926,-5.8546,0.92609,-0.37568,-0.034996,65.933,0.37535,0.92675,-0.015886,-77.078 > view matrix models > #28,0.75378,0.65514,-0.051086,-44.642,-0.54582,0.58092,-0.60384,218.55,-0.36592,0.48304,0.79547,-29.499 > view matrix models > #28,0.93053,0.32568,-0.16747,-7.3436,-0.34314,0.93516,-0.087963,68.823,0.12796,0.13932,0.98195,-76.969 > ui mousemode right ""translate selected models"" > view matrix models > #28,0.93053,0.32568,-0.16747,-12.031,-0.34314,0.93516,-0.087963,69.72,0.12796,0.13932,0.98195,-23.264 > select subtract #28 Nothing selected > fitmap #28 inMap #26 Fit map cryosparc_P4_J257_002_volume_map_sharp.mrc z flip in map CS_P4_J256_sharp_flip.mrc using 5113 points correlation = 0.961, correlation about mean = 0.8355, overlap = 1.813e+04 steps = 76, shift = 3.44, angle = 10.7 degrees Position of cryosparc_P4_J257_002_volume_map_sharp.mrc z flip (#28) relative to CS_P4_J256_sharp_flip.mrc (#26) coordinates: Matrix rotation and translation 0.99983973 0.00266136 0.01770477 -3.60430289 -0.00275366 0.99998275 0.00519130 -0.72993632 -0.01769065 -0.00523922 0.99982979 3.00234542 Axis -0.27967225 0.94905354 -0.14519233 Axis point 166.73187411 0.00000000 206.99324341 Rotation angle (degrees) 1.06849905 Shift along axis -0.12064266 > rename #28 CS_P4_J257_sharp_flip id #27 > save CS_P4_J257_sharp_flip.mrc #27 > hide #!26 models > hide #!27 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J258_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J258_002_volume_map_sharp.mrc as #28, grid size 80,80,80, pixel 3.32, shown at level 0.533, step 1, values float32 > select add #28 2 models selected > show #!27 models > view matrix models #28,1,0,0,2.9293,0,1,0,12.799,0,0,1,30.196 > ui mousemode right ""rotate selected models"" > view matrix models > #28,-0.94564,-0.32466,0.018849,316.84,-0.32175,0.94244,0.090998,54.708,-0.047307,0.079987,-0.99567,265.03 > select up 56 models selected > select up 56 models selected > select down 2 models selected > select down 2 models selected > select subtract #28 Nothing selected > hide #!27 models > volume flip #28 Opened cryosparc_P4_J258_002_volume_map_sharp.mrc z flip as #29, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #28 > select add #29 2 models selected > view matrix models > #29,0.95822,0.27409,-0.081793,-16.892,-0.27702,0.96049,-0.026814,62.796,0.071212,0.048352,0.99629,-31.428 > show #!27 models > select subtract #29 Nothing selected > fitmap #29 inMap #27 Fit map cryosparc_P4_J258_002_volume_map_sharp.mrc z flip in map CS_P4_J257_sharp_flip.mrc using 5117 points correlation = 0.4043, correlation about mean = 0.1105, overlap = 1145 steps = 104, shift = 9.56, angle = 9.45 degrees Position of cryosparc_P4_J258_002_volume_map_sharp.mrc z flip (#29) relative to CS_P4_J257_sharp_flip.mrc (#27) coordinates: Matrix rotation and translation 0.98218261 0.18784329 -0.00567361 -27.82492616 -0.18685004 0.97932905 0.07747035 28.59524537 0.02010861 -0.07502992 0.99697851 -24.36927466 Axis -0.37621012 -0.06360338 -0.92434872 Axis point 152.56947582 100.16313614 0.00000000 Rotation angle (degrees) 11.69370116 Shift along axis 31.17497259 > select add #29 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #29,0.91472,0.40193,-0.041674,-52.044,-0.39883,0.91458,0.066882,60.074,0.064997,-0.044558,0.99689,0.70588 > view matrix models > #29,0.91472,0.40193,-0.041674,-39.705,-0.39883,0.91458,0.066882,54.066,0.064997,-0.044558,0.99689,6.2725 > fitmap #29 inMap #27 Fit map cryosparc_P4_J258_002_volume_map_sharp.mrc z flip in map CS_P4_J257_sharp_flip.mrc using 5117 points correlation = 0.8335, correlation about mean = 0.5457, overlap = 5135 steps = 64, shift = 1.52, angle = 12.1 degrees Position of cryosparc_P4_J258_002_volume_map_sharp.mrc z flip (#29) relative to CS_P4_J257_sharp_flip.mrc (#27) coordinates: Matrix rotation and translation 0.99996433 -0.00752131 -0.00383843 1.74823892 0.00752090 0.99997170 -0.00012121 -0.88867123 0.00383923 0.00009234 0.99999262 -0.68815928 Axis 0.01264381 -0.45457780 0.89061729 Axis point 130.32470586 232.13443622 0.00000000 Rotation angle (degrees) 0.48385831 Shift along axis -0.18681194 > select subtract #29 Nothing selected > rename #29 CS_P4_J258_sharp_flip id #28 > save CS_P4_J258_sharp_flip.mrc #28 > hide #!27 models > hide #!28 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J259_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J259_002_volume_map_sharp.mrc as #29, grid size 80,80,80, pixel 3.32, shown at level 0.567, step 1, values float32 > select add #29 2 models selected > show #!28 models > view matrix models #29,1,0,0,-4.0284,0,1,0,3.9973,0,0,1,26.374 > ui mousemode right ""rotate selected models"" > view matrix models > #29,0.37373,0.91624,0.14434,-63.019,0.92743,-0.36674,-0.073343,74.867,-0.014266,0.16128,-0.98681,258.72 > view matrix models > #29,0.2129,0.93735,0.27578,-60.698,0.97539,-0.1873,-0.11636,49.108,-0.057419,0.29377,-0.95415,242.23 > hide #!28 models > select subtract #29 Nothing selected > volume flip #29 Opened cryosparc_P4_J259_002_volume_map_sharp.mrc z flip as #30, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #29 > select add #30 2 models selected > show #!28 models > view matrix models > #30,0.90176,0.31537,-0.29559,8.3185,-0.32745,0.94483,0.0091223,54.046,0.28216,0.088565,0.95527,-34.506 > select subtract #30 Nothing selected > fitmap #30 inMap #28 Fit map cryosparc_P4_J259_002_volume_map_sharp.mrc z flip in map CS_P4_J258_sharp_flip.mrc using 5112 points correlation = 0.9666, correlation about mean = 0.6628, overlap = 3020 steps = 80, shift = 5.99, angle = 15.1 degrees Position of cryosparc_P4_J259_002_volume_map_sharp.mrc z flip (#30) relative to CS_P4_J258_sharp_flip.mrc (#28) coordinates: Matrix rotation and translation 0.99996699 0.00262374 -0.00768921 0.94371527 -0.00261765 0.99999625 0.00080251 0.08556771 0.00769129 -0.00078235 0.99997011 -0.47262490 Axis -0.09707497 -0.94207663 -0.32104217 Axis point 62.77947672 0.00000000 122.20423531 Rotation angle (degrees) 0.46771540 Shift along axis -0.02048995 > rename #30 CS_P4_J259_sharp_flip id #29 > save CS_P4_J259_sharp_flip.mrc #29 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260502_SA-F_B1_workflow.cxs"" > hide #!29 models > hide #!28 models > show #!25 models > color #25 #FCEDFF > hide #!25 models > show #!28 models > color #28 #FCEDFF > hide #!28 models > show #!29 models > color #29 #FCEDFF > hide #!29 models > show #!29 models > show #!26 models > hide #!29 models > color #26 #99BFE5 > hide #!26 models > show #!27 models > color #27 #99BFE5 > view P1 > hide #!27 models > show #!25 models > ui mousemode right ""translate selected models"" > ui mousemode right translate > view P1 > save CS_P4_J255_NU_sharp.png supersample 3 transparentBackground true > hide #!25 models > show #!26 models > volume #26 level 1.012 > save CS_P4_J256_NU_sharp.png supersample 3 transparentBackground true > hide #!26 models > show #!27 models > save CS_P4_J257_NU_sharp.png supersample 3 transparentBackground true > hide #!27 models > show #!28 models > save CS_P4_J258_NU_sharp.png supersample 3 transparentBackground true > hide #!28 models > show #!29 models > save CS_P4_J259_NU_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260502_SA-F_B1_workflow.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J285_006_volume_map_sharp.mrc"" Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.0363, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J267_008_volume_map_sharp.mrc"" Opened cryosparc_P4_J267_008_volume_map_sharp.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.0747, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J277_008_volume_map_sharp.mrc"" Opened cryosparc_P4_J277_008_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0762, step 2, values float32 > hide #!29 models > hide #!30 models > hide #!31 models > show #!31 models > hide #!32 models > show #!30 models > close #30 > show #!27 models > select add #31 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #31,-0.90396,0.26529,0.33537,196.37,0.29187,0.95597,0.030503,-41.724,-0.31251,0.12546,-0.94159,315.51 > hide #!27 models > view matrix models > #31,-0.95736,-0.095902,0.27253,266.49,-0.06692,0.99125,0.11374,-5.5307,-0.28105,0.090649,-0.9554,317.94 > show #!29 models > hide #!29 models > select subtract #31 Nothing selected > close #32 > volume flip #31 Opened cryosparc_P4_J267_008_volume_map_sharp.mrc z flip as #30, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #30 > show #!31 models > select add #31 2 models selected > show #!27 models > ui mousemode right ""translate selected models"" > view matrix models > #31,-0.95736,-0.095902,0.27253,258.1,-0.06692,0.99125,0.11374,14.401,-0.28105,0.090649,-0.9554,295.97 > ui mousemode right ""rotate selected models"" > view matrix models > #31,0.57983,0.79903,0.15922,-85.975,0.81408,-0.57604,-0.073785,139.64,0.032763,0.1724,-0.98448,241.38 > ui mousemode right ""translate selected models"" > view matrix models > #31,0.57983,0.79903,0.15922,-74.26,0.81408,-0.57604,-0.073785,114.14,0.032763,0.1724,-0.98448,243.66 > ui mousemode right ""rotate selected models"" > view matrix models > #31,0.38773,0.91358,0.12259,-56.869,0.92165,-0.3821,-0.067497,68.753,-0.014823,0.13915,-0.99016,256.48 > ui mousemode right ""translate selected models"" > view matrix models > #31,0.38773,0.91358,0.12259,-59.17,0.92165,-0.3821,-0.067497,73.776,-0.014823,0.13915,-0.99016,255.81 > fitmap #31 inMap #27 Fit map cryosparc_P4_J267_008_volume_map_sharp.mrc in map CS_P4_J257_sharp_flip.mrc using 40948 points correlation = 0.4368, correlation about mean = 0.04808, overlap = 2838 steps = 84, shift = 6.03, angle = 16 degrees Position of cryosparc_P4_J267_008_volume_map_sharp.mrc (#31) relative to CS_P4_J257_sharp_flip.mrc (#27) coordinates: Matrix rotation and translation -0.09805932 0.98945486 0.10659935 2.84911711 0.99008140 0.10782511 -0.09006967 -2.59568012 -0.10061396 0.09670986 -0.99021412 262.50076525 Axis 0.66953234 0.74277951 0.00224590 Axis point 14.97851108 -0.00000000 131.13786872 Rotation angle (degrees) 171.98194915 Shift along axis 0.56910865 > select subtract #31 Nothing selected > hide #!31 models > hide #!27 models > show #!31 models > close #31 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J267_008_volume_map_sharp.mrc"" Opened cryosparc_P4_J267_008_volume_map_sharp.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.0747, step 2, values float32 > select add #30 2 models selected > show #!27 models > ui mousemode right ""rotate selected models"" > view matrix models > #30,0.59059,-0.80637,-0.031153,183.8,-0.80688,-0.59066,-0.008015,354.56,-0.011937,0.02987,-0.99948,293.1 > ui mousemode right ""translate selected models"" > view matrix models > #30,0.59059,-0.80637,-0.031153,187.84,-0.80688,-0.59066,-0.008015,342.67,-0.011937,0.02987,-0.99948,267.57 > hide #!27 models > show #!27 models > hide #!30 models > hide #!27 models > show #!30 models > volume flip #30 Opened cryosparc_P4_J267_008_volume_map_sharp.mrc z flip as #31, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > select subtract #30 Nothing selected > close #30 > select add #31 2 models selected > show #!27 models > view matrix models > #31,0.59059,-0.80637,-0.031153,181.08,-0.80688,-0.59066,-0.008015,342.68,-0.011937,0.02987,-0.99948,285.6 > ui mousemode right ""rotate selected models"" > view matrix models > #31,0.49825,-0.85813,0.12394,182.63,-0.032454,0.12438,0.9917,19.314,-0.86642,-0.49814,0.034125,354.11 > view matrix models > #31,-0.47795,-0.87619,-0.061991,343.39,0.85267,-0.47976,0.20686,70.492,-0.21099,0.046011,0.9764,77.316 > ui mousemode right ""translate selected models"" > view matrix models > #31,-0.47795,-0.87619,-0.061991,322.39,0.85267,-0.47976,0.20686,71.691,-0.21099,0.046011,0.9764,36.515 > view matrix models > #31,-0.47795,-0.87619,-0.061991,329.78,0.85267,-0.47976,0.20686,58.248,-0.21099,0.046011,0.9764,36.244 > fitmap #31 inMap #27 Fit map cryosparc_P4_J267_008_volume_map_sharp.mrc z flip in map CS_P4_J257_sharp_flip.mrc using 327854 points correlation = 0.6967, correlation about mean = 0.2684, overlap = 4.49e+04 steps = 92, shift = 8.63, angle = 16.2 degrees Position of cryosparc_P4_J267_008_volume_map_sharp.mrc z flip (#31) relative to CS_P4_J257_sharp_flip.mrc (#27) coordinates: Matrix rotation and translation -0.48810574 -0.85845883 -0.15748400 338.09346066 0.86132304 -0.50293557 0.07196129 74.97027819 -0.14098011 -0.10051988 0.98489611 32.48936744 Axis -0.09978729 -0.00954816 0.99496298 Axis point 149.01931346 135.27108975 0.00000000 Rotation angle (degrees) 120.20349080 Shift along axis -2.12754240 > select subtract #31 Nothing selected > volume #27 level 1.164 > volume #31 level 0.1055 > hide #!27 models > volume #31 level 0.1343 > color #31 #99BFE5 > rename #31 CS_P4_J267_sharp_flip id #30 > save CS_P4_J267_sharp_flip.mrc #30 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J277_008_volume_map_sharp.mrc"" Opened cryosparc_P4_J277_008_volume_map_sharp.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.0762, step 2, values float32 > hide #!30 models > select add #31 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #31,0.50169,-0.77701,0.38022,112.38,-0.8444,-0.53533,0.020189,301.01,0.18786,-0.33119,-0.92467,273.22 > view matrix models > #31,0.77218,-0.62718,0.10187,94.664,-0.63536,-0.764,0.11236,288.83,0.0073633,-0.15149,-0.98843,283.82 > volume flip #31 Opened cryosparc_P4_J277_008_volume_map_sharp.mrc z flip as #32, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #31 > select add #32 2 models selected > show #!30 models > view matrix models > #32,0.90608,0.27127,-0.3247,15.596,-0.28323,0.95899,0.010829,28.44,0.31432,0.082155,0.94575,-47.16 > view matrix models > #32,0.99239,-0.018676,-0.12173,15.559,0.019459,0.9998,0.0052468,-15.401,0.1216,-0.0075755,0.99255,-16.612 > ui mousemode right ""translate selected models"" > view matrix models > #32,0.99239,-0.018676,-0.12173,21.14,0.019459,0.9998,0.0052468,-2.6957,0.1216,-0.0075755,0.99255,-9.4459 > fitmap #32 inMap #30 Fit map cryosparc_P4_J277_008_volume_map_sharp.mrc z flip in map CS_P4_J267_sharp_flip.mrc using 327711 points correlation = 0.7196, correlation about mean = 0.3385, overlap = 5671 steps = 204, shift = 3.68, angle = 13.7 degrees Position of cryosparc_P4_J277_008_volume_map_sharp.mrc z flip (#32) relative to CS_P4_J267_sharp_flip.mrc (#30) coordinates: Matrix rotation and translation -0.48144357 0.86501463 -0.14128627 103.86408789 -0.86432037 -0.49531179 -0.08727288 328.52215562 -0.14547307 0.08009963 0.98611442 10.75546195 Axis 0.09633390 0.00240978 -0.99534616 Axis point 148.32654443 133.96556119 0.00000000 Rotation angle (degrees) 119.69088439 Shift along axis 0.09189113 > select subtract #32 Nothing selected > volume #32 level 0.1306 > hide #!30 models > volume #32 level 0.1432 > color #32 #99BFE5 > rename #32 CS_P4_J277_sharp_flip id #31 > save CS_P4_J277_sharp_flip.mrc #31 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J285_006_volume_map_sharp.mrc"" Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0363, step 2, values float32 > hide #!31 models > select add #32 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #32,0.30706,0.95043,0.049005,-33.318,0.9497,-0.30268,-0.080397,47.411,-0.061579,0.071226,-0.99556,261.24 > volume flip #32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #33, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > show #!31 models > show #!32 models > view matrix models > #32,0.19586,0.82677,-0.52734,72.951,0.95192,-0.28947,-0.10029,48.053,-0.23556,-0.48235,-0.84371,334.74 > view matrix models > #32,0.038463,0.98737,0.15371,-15.568,0.97818,-0.0057722,-0.20769,22.74,-0.20418,0.15835,-0.96604,265.55 > close #32 > select add #33 2 models selected > view matrix models > #33,-0.36526,-0.91739,-0.15805,324.89,0.9276,-0.34439,-0.14472,64.223,0.078335,-0.19947,0.97677,17.619 > view matrix models > #33,-0.3296,-0.92737,-0.17708,323.89,0.91639,-0.35937,0.17633,25.386,-0.22716,-0.10416,0.96827,47.503 > select subtract #33 Nothing selected > fitmap #33 inMap #31 Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map CS_P4_J277_sharp_flip.mrc using 327344 points correlation = 0.3754, correlation about mean = 0.04431, overlap = 1099 steps = 64, shift = 4.4, angle = 1.24 degrees Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative to CS_P4_J277_sharp_flip.mrc (#31) coordinates: Matrix rotation and translation -0.52307807 -0.83656982 -0.16291178 338.77635518 0.81824450 -0.54640858 0.17864376 66.60900444 -0.23846438 -0.03985703 0.97033300 35.38091339 Axis -0.13076939 0.04521708 0.99038113 Axis point 153.51682890 124.48577590 0.00000000 Rotation angle (degrees) 123.33798629 Shift along axis -6.24912375 > volume #33 level 0.05666 > select add #33 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #33,-0.32295,-0.92807,-0.18543,326.53,0.9135,-0.3569,0.19529,26.322,-0.24742,-0.10632,0.96306,60.406 > fitmap #33 inMap #31 Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map CS_P4_J277_sharp_flip.mrc using 194771 points correlation = 0.7316, correlation about mean = 0.2783, overlap = 2429 steps = 104, shift = 3.72, angle = 6.69 degrees Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative to CS_P4_J277_sharp_flip.mrc (#31) coordinates: Matrix rotation and translation -0.48329817 -0.86312458 -0.14641999 335.54076959 0.86340511 -0.49758655 0.08330200 72.08568886 -0.14475663 -0.08616006 0.98570885 33.43360614 Axis -0.09768239 -0.00095880 0.99521718 Axis point 148.43445219 133.71191357 0.00000000 Rotation angle (degrees) 119.84054702 Shift along axis 0.42815717 > select subtract #33 Nothing selected > select add #33 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #33,-0.6364,0.75107,-0.17577,140.89,-0.74512,-0.6575,-0.11171,345.32,-0.19948,0.059876,0.97807,29.849 > ui mousemode right ""translate selected models"" > view matrix models > #33,-0.6364,0.75107,-0.17577,136.82,-0.74512,-0.6575,-0.11171,338.86,-0.19948,0.059876,0.97807,29.687 > ui mousemode right ""rotate selected models"" > view matrix models > #33,-0.73358,0.64738,-0.20678,168.84,-0.63708,-0.76101,-0.12246,339.46,-0.23664,0.041901,0.97069,38.344 > fitmap #33 inMap #31 Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map CS_P4_J277_sharp_flip.mrc using 194771 points correlation = 0.4346, correlation about mean = 0.05784, overlap = 1046 steps = 96, shift = 4.05, angle = 4.16 degrees Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative to CS_P4_J277_sharp_flip.mrc (#31) coordinates: Matrix rotation and translation -0.58502424 0.80932802 -0.05229508 107.72395607 -0.80221021 -0.58694418 -0.10934029 332.49911712 -0.11918646 -0.02201508 0.99262777 22.68232922 Axis 0.05406170 0.04141143 -0.99767852 Axis point 139.16943260 139.24984383 0.00000000 Rotation angle (degrees) 126.13361686 Shift along axis -3.03667024 > ui mousemode right ""translate selected models"" > view matrix models > #33,-0.7311,0.66788,-0.13939,159.58,-0.65889,-0.74418,-0.10984,339.55,-0.17709,0.011538,0.98413,33.11 > fitmap #33 inMap #31 Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map CS_P4_J277_sharp_flip.mrc using 194771 points correlation = 0.7261, correlation about mean = 0.2429, overlap = 2435 steps = 148, shift = 3.57, angle = 8.91 degrees Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative to CS_P4_J277_sharp_flip.mrc (#31) coordinates: Matrix rotation and translation -0.47691102 0.86730315 -0.14262219 103.16958211 -0.86637561 -0.49120809 -0.09004393 328.47939238 -0.14815256 0.08062145 0.98567285 11.48812128 Axis 0.09796714 0.00317460 -0.99518459 Axis point 148.54824739 133.97305983 0.00000000 Rotation angle (degrees) 119.42100612 Shift along axis -0.28278057 > ui mousemode right ""rotate selected models"" > view matrix models > #33,0.98687,0.16137,0.0076046,-28.356,-0.15803,0.97406,-0.16197,41.243,-0.033544,0.15864,0.98677,-7.5792 > ui mousemode right ""translate selected models"" > view matrix models > #33,0.98687,0.16137,0.0076046,-22.398,-0.15803,0.97406,-0.16197,51.235,-0.033544,0.15864,0.98677,-4.7399 > fitmap #33 inMap #31 Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map CS_P4_J277_sharp_flip.mrc using 194771 points correlation = 0.9896, correlation about mean = 0.9159, overlap = 4214 steps = 120, shift = 4.17, angle = 9.65 degrees Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative to CS_P4_J277_sharp_flip.mrc (#31) coordinates: Matrix rotation and translation 0.99997973 -0.00439362 0.00460748 -0.02530815 0.00439161 0.99999024 0.00044636 -0.51759472 -0.00460939 -0.00042611 0.99998927 1.01725436 Axis -0.06835965 0.72216012 0.68833983 Axis point 171.68283436 0.00000000 1.37920014 Rotation angle (degrees) 0.36563312 Shift along axis 0.32816049 > select subtract #33 Nothing selected > hide #!31 models > show #!31 models > hide #!31 models > volume #33 level 0.06481 > color #33 #99BFE5 > view P1 > rename #33 CS_P4_J285_sharp_flip id #32 > save CS_P4_J285_sharp_flip.mrc #32 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260502_SA-F_B1_workflow.cxs"" > save CS_P4_J285_NU_sharp.png supersample 3 transparentBackground true > hide #!32 models > show #!31 models > save CS_P4_J277_NU_sharp.png supersample 3 transparentBackground true > hide #!31 models > show #!30 models > save CS_P4_J267_NU_sharp.png supersample 3 transparentBackground true > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J282_005_volume_map_sharp.mrc"" Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32 > select add #33 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #33,0.77382,-0.58736,0.23709,68.017,-0.6199,-0.77915,0.092993,287.71,0.13011,-0.21893,-0.96703,293.89 > volume flip sel Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #34, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > select subtract #33 Nothing selected > select add #34 2 models selected > view matrix models > #34,0.96024,0.18105,-0.2125,4.9844,-0.18441,0.98284,0.0040821,22.146,0.20959,0.035266,0.97715,4.1522 > volume #34 level 0.06153 > ui mousemode right ""translate selected models"" > view matrix models > #34,0.96024,0.18105,-0.2125,5.3992,-0.18441,0.98284,0.0040821,24.944,0.20959,0.035266,0.97715,-19.851 > fitmap #34 inMap #30 Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map CS_P4_J267_sharp_flip.mrc using 179913 points correlation = 0.7668, correlation about mean = 0.2691, overlap = 2384 steps = 132, shift = 4.76, angle = 10.2 degrees Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#34) relative to CS_P4_J267_sharp_flip.mrc (#30) coordinates: Matrix rotation and translation -0.47859383 0.86460690 -0.15297990 105.65226772 -0.86128787 -0.49615211 -0.10961884 331.90892973 -0.17067851 0.07929683 0.98213077 14.98614385 Axis 0.10880400 0.01019333 -0.99401096 Axis point 150.51207819 135.19673705 0.00000000 Rotation angle (degrees) 119.75601097 Shift along axis -0.01774616 > select subtract #34 Nothing selected > select add #34 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #34,-0.29858,-0.92833,-0.22151,340.08,0.93935,-0.32688,0.10377,36.917,-0.16874,-0.17709,0.96962,60.484 > fitmap #34 inMap #30 Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map CS_P4_J267_sharp_flip.mrc using 179913 points correlation = 0.4184, correlation about mean = 0.03499, overlap = 815.8 steps = 72, shift = 3.19, angle = 2.56 degrees Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#34) relative to CS_P4_J267_sharp_flip.mrc (#30) coordinates: Matrix rotation and translation 0.99975679 -0.00914856 -0.02006678 -0.29483780 0.00937915 0.99989072 0.01142689 -12.23865962 0.01996005 -0.01161232 0.99973334 -0.12571505 Axis -0.46299067 -0.80436995 0.37232865 Axis point 194.44052306 0.00000000 212.15518455 Rotation angle (degrees) 1.42571524 Shift along axis 9.93410983 > ui mousemode right ""translate selected models"" > view matrix models > #34,-0.29149,-0.93644,-0.19523,323.34,0.9479,-0.31019,0.07257,35.755,-0.12852,-0.16391,0.97807,48.671 > fitmap #34 inMap #30 Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map CS_P4_J267_sharp_flip.mrc using 179913 points correlation = 0.9696, correlation about mean = 0.7683, overlap = 3705 steps = 76, shift = 2.39, angle = 2.68 degrees Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#34) relative to CS_P4_J267_sharp_flip.mrc (#30) coordinates: Matrix rotation and translation 0.99970034 -0.00006024 0.02447927 -4.11138943 0.00004629 0.99999984 0.00057062 0.05899118 -0.02447930 -0.00056932 0.99970018 3.40337319 Axis -0.02327752 0.99972667 0.00217546 Axis point 136.94050248 0.00000000 169.47617625 Rotation angle (degrees) 1.40308329 Shift along axis 0.16208189 > select subtract #34 Nothing selected > hide #!30 models > show #!32 models > hide #!31 models > volume #34 level 0.06805 > hide #!32 models > view P1 > close #33 > rename #34 CS_P4_J282_sharp_flip id #33 > save CS_P4_J282_sharp_flip.mrc #33 > view P1 > save CS_P4_J282_NU_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260502_SA-F_B1_workflow1.cxs"" > color #33 #99BFE5 > save CS_P4_J282_NU_sharp1.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260502_SA-F_B1_workflow1.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J287_map_locres.mrc"" Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 9.77, step 2, values float32 > rename #34 cryosparc_P4_J287_map_locres_forJ282 > select add #34 2 models selected > view matrix models #34,1,0,0,-1.0935,0,1,0,0.90366,0,0,1,6.3532 > ui mousemode right ""rotate selected models"" > view matrix models > #34,0.41458,0.88648,0.20563,-71.892,0.90978,-0.4089,-0.07146,80.866,0.020734,0.2167,-0.97602,247.42 > view matrix models > #34,0.40248,0.89866,0.17442,-67.589,0.91533,-0.39227,-0.091056,80.514,-0.013407,0.1963,-0.98045,255.56 > view matrix models > #34,0.3547,0.92587,0.13022,-58.659,0.93218,-0.33944,-0.12576,75.687,-0.072238,0.166,-0.98348,268.27 > fitmap #34 inMap #33 Fit map cryosparc_P4_J287_map_locres_forJ282 in map CS_P4_J282_sharp_flip.mrc using 40893 points correlation = 0.2997, correlation about mean = 0.02148, overlap = 2955 steps = 140, shift = 9.61, angle = 2.61 degrees Position of cryosparc_P4_J287_map_locres_forJ282 (#34) relative to CS_P4_J282_sharp_flip.mrc (#33) coordinates: Matrix rotation and translation 0.77162333 -0.63598985 0.01069393 118.29154644 -0.63440309 -0.76826072 0.08548800 317.77796206 -0.04615378 -0.07274879 -0.99628182 298.10083492 Axis -0.94106809 0.33808548 0.00943679 Axis point 0.00000000 186.80747823 142.52542945 Rotation angle (degrees) 175.17728056 Shift along axis -1.07117046 > volume #34 level 6.762 > view matrix models > #34,0.42433,0.90126,0.087581,-65.663,0.89997,-0.40908,-0.15069,88.731,-0.099987,0.14276,-0.98469,281 > ui mousemode right ""translate selected models"" > view matrix models > #34,0.42433,0.90126,0.087581,-62.736,0.89997,-0.40908,-0.15069,86.303,-0.099987,0.14276,-0.98469,272.65 > view matrix models > #34,0.42433,0.90126,0.087581,-62.591,0.89997,-0.40908,-0.15069,86.167,-0.099987,0.14276,-0.98469,272.2 > volume #34 level 6.762 > volume #34 level 6.47 > ui tool show ""Surface Color"" > color sample #33.1 map #34 palette #ff0000:#ffffff:#0000ff outsideColor > #808080 Map values for surface ""surface"": minimum 0, mean 4.349, maximum 40.76 > select subtract #34 Nothing selected > hide #!34 models > key red-white-blue :0.0 :20.4 :40.8 showTool true > ui mousemode right ""color key"" > key red-white-blue :0.0 :20.4 :40.8 white: > key red:0.0 white:20.4 blue:40.8 white: white: > key red:0.0 white:20.4 blue:40.8 white: > key red-white-blue :0.0 :20.4 :40.8 > key red-white-blue :0 :2 :4 showTool true > ui mousemode right ""color key"" > key red-white-blue :0 :2 :4 white: > key red:0 white:2 blue:4 white: white: > color single #33.1 > color sample #33.1 map #34 palette 0,#ff0000:2,#ffffff:4,#0000ff > outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.349, maximum 40.76 > key red-white-blue :0 :2 :4 showTool true > ui mousemode right ""color key"" > key red-white-blue :0 :2 :4 showTool true > key red-white-blue :0 :2 :4 white: > key red:0 white:2 blue:4 white: white: > key red:0 white:2 blue:4 white: white:0 > key red:0 white:2 blue:4 white:1 white:0 > key red:0 white:2 blue:2 white:1 white:0 > key red:0 white:3 blue:2 white:1 white:0 > key red:4 white:3 blue:2 white:1 white:0 > key gnbu :4 :3 :2 :1 :0 > key esmfold :4 :3 :2 :1 :0 > key dark2-5 :4 :3 :2 :1 :0 > key pastel1-5 :4 :3 :2 :1 :0 > key blues :4 :3 :2 :1 :0 > key accent-5 :4 :3 :2 :1 :0 > color sample #33.1 map #34 palette 0,#ff0000:2,#ffffff:4,#0000ff > outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.349, maximum 40.76 > color sample #33.1 map #34 palette 0,#ff0000:2,#ffffff:4,#0000ff > outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.349, maximum 40.76 > color sample #33.1 map #34 palette 0,#0000ff:2,#7f7fff:4,#ffffff > outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.349, maximum 40.76 > key blue:0 #7f7fff:2 white:4 showTool true > ui mousemode right ""color key"" > key blue:0 #7f7fff:2 white:4 showTool true > key blue:0 #7f7fff:2 white:4 white: > key blue:0 #7f7fff:2 white:4 white: white: > color sample #33.1 map #34 palette > 0,#0000ff:1,#7f7fff:2,#ffffff:3,#ff7f7f:4,#ff0000 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.349, maximum 40.76 > key blue:0 #7f7fff:1 white:2 #ff7f7f:3 red:4 showTool true > ui mousemode right ""color key"" > color sample #33.1 map #34 palette > 0,#0000ff:1,#7f7fff:2,#ffffff:3,#ff7f7f:4,#ff0000 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.349, maximum 40.76 > color sample #33.1 map #34 palette > 0,#ff0000:1,#ff7f7f:2,#ffffff:3,#7f7fff:4,#0000ff outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.349, maximum 40.76 > color sample #33.1 map #34 palette > 0,#ff0000:2,#ff7f7f:4,#ffffff:5,#7f7fff:8,#0000ff outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.349, maximum 40.76 > volume #33 level 0.08574 > key red:0 #ff7f7f:2 white:4 #7f7fff:5 blue:8 showTool true > key red:0 #ff7f7f:2 white:4 #7f7fff:6 blue:8 showTool true > color sample #33.1 map #34 palette > 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ff7f7f:8,#ff0000 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.269, maximum 35.43 > color sample #33.1 map #34 palette > 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ff7f7f:8,#fff6c0 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.269, maximum 35.43 > key blue:0 #7f7fff:2 white:4 #ff7f7f:6 #fff6c0:8 showTool true > color sample #33.1 map #34 palette > 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ffad7f:8,#fff6c0 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.269, maximum 35.43 > color sample #33.1 map #34 palette > 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.269, maximum 35.43 > key blue:0 #7f7fff:2 white:4 #ff967f:6 #fff6c0:8 showTool true > color sample #33.1 map #34 palette > 0,#fff6c0:2,#ff967f:4,#ffffff:6,#7f7fff:8,#0000ff outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.269, maximum 35.43 > color sample #33.1 map #34 palette > 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.269, maximum 35.43 > key blue:0 #7f7fff:2 white:4 #ff967f:6 #fff6c0:8 showTool true > color sample #33.1 map #34 palette > 0,#00a7ff:2,#7f7fff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.269, maximum 35.43 > key #00a7ff:0 #7f7fff:2 white:4 #ff967f:6 #fff6c0:8 showTool true > color sample #33.1 map #34 palette > 0,#00a7ff:2,#d2a5ff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.269, maximum 35.43 > key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260502_SA-F_B1_workflow2.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J288_map_locres.mrc"" Opened cryosparc_P4_J288_map_locres.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 8.93, step 2, values float32 > hide #35 models > show #35 models > hide #!36 models > hide #!33 models > show #!33 models > rename #36 cryosparc_P4_J288_map_locres_forJ285 > hide #!33 models > show #!32 models > hide #35 models > show #!36 models > select add #36 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #36,0.54984,-0.77769,0.30476,129.28,-0.81459,-0.57994,-0.010221,331.17,0.18469,-0.24264,-0.95237,263.23 > ui mousemode right ""translate selected models"" > view matrix models > #36,0.54984,-0.77769,0.30476,119.97,-0.81459,-0.57994,-0.010221,318.58,0.18469,-0.24264,-0.95237,280.96 > volume #36 level 6.234 > select subtract #36 Nothing selected > ui tool show ""Surface Color"" > color sample #32.1 map #36 palette > 0,#00a7ff:2,#d2a5ff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > hide #!36 models > show #!33 models > hide #!33 models > show #!33 models > hide #!32 models > show #!32 models > hide #!33 models > key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true > show #!36 models > hide #!36 models > key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 white: > key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 Fetching compressed palette custom from https://www.colourlovers.com/api/palettes?keywords=custom&format=json&numResults=100 Could not find palette custom at COLOURlovers.com using keyword search > color sample #32.1 map #36 palette > 0,#00a7ff:2,#d2a5ff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true > hide #!32 models > show #35 models > show #!32 models > select add #35 1 model selected > view matrix models #35,1,0,0,-1.208,0,1,0,-1.3654,0,0,1,1.1486 > select subtract #35 Nothing selected > select add #35 1 model selected > select subtract #35 Nothing selected > key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true > ui mousemode right ""color key"" > select add #35 1 model selected > show #35 > view W35 Expected an objects specifier or a view name or a keyword > view #35 No displayed objects specified. > close #35 > key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true > ui mousemode right ""color key"" > hide #!32 models > show #!33 models > hide #!33 models > show #!33 models > hide #!33 models > show #!33 models > volume #33 level 0.06991 > hide #!33 models > show #!32 models > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260502_SA-F_B1_workflow2.cxs"" > color sample #32.1 map #36 palette > 0,#00a7ff:2,#99bfe5:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > key #00a7ff:0 #99bfe5:2 white:4 #fff6c0:6 #ff967f:8 showTool true > ui mousemode right ""color key"" > color sample #32.1 map #36 palette > 0,#00a7ff:2,#99bfe5:4,#ffffff:6,#fff6c0:8,#ff967f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#d2a5ff:2,#99bfe5:4,#ffffff:6,#fff6c0:8,#ff967f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > key #d2a5ff:0 #99bfe5:2 white:4 #fff6c0:6 #ff967f:8 showTool true > view #35 No objects specified. > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#99bfe5:4,#ffffff:6,#fff6c0:8,#ff967f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > key #e7c4ff:0 #99bfe5:2 white:4 #fff6c0:6 #ff967f:8 showTool true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260502_SA-F_B1_workflow2.cxs"" > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#99bfe5:4,#5da0ff:6,#fff6c0:8,#ff967f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#e0bfe8:4,#99bfe5:6,#fff6c0:8,#ff967f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#e0dee8:4,#99bfe5:6,#fff6c0:8,#ff967f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#e0dee8:4,#99bfe5:6,#fff6c0:8,#ff967f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#6676ed:4,#99bfe5:6,#fff6c0:8,#ff967f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#6676ed:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#99bfe5:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#99bfe5:4,#6676ed:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#99bfe5:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#799bea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#5756ea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#ffdedd:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#ffc9a3:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#ffb17f:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > key #ffb17f:0 #527dea:2 #99bfe5:4 #fff6c0:6 #f4fff3:8 showTool true > ui mousemode right ""color key"" > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260502_SA-F_B1_workflow3.cxs"" > hide #!32 models > show #!33 models > hide #!33 models > show #!32 models > hide #!32 models > show #!33 models > hide #!33 models > show #!32 models > volume #34 step 1 > volume #36 step 1 > show #!36 models > volume flip #36 Opened cryosparc_P4_J288_map_locres_forJ285 z flip as #38, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > hide #37 models > ui mousemode right ""rotate selected models"" > hide #!32 models > show #!32 models > hide #!38 models > show #!38 models > select add #38 2 models selected > view matrix models > #38,-0.22965,0.94651,-0.22667,61.099,-0.95753,-0.26145,-0.12161,309.34,-0.17437,0.18912,0.96635,13.289 > view matrix models > #38,-0.47581,-0.84028,-0.25987,345.82,0.86453,-0.50117,0.037622,69.811,-0.16185,-0.20677,0.96491,66.334 > view matrix models > #38,-0.72836,0.6263,-0.27792,180.88,-0.55109,-0.77649,-0.30556,349.01,-0.40718,-0.069403,0.91071,88.496 > view matrix models > #38,-0.422,0.88275,-0.20657,93.707,-0.7937,-0.46985,-0.38638,351.04,-0.43814,0.0009021,0.89891,84.657 > fitmap #38 inMap #32 Fit map cryosparc_P4_J288_map_locres_forJ285 z flip in map CS_P4_J285_sharp_flip.mrc using 1112104 points correlation = 0.2781, correlation about mean = -0.02765, overlap = 7.665e+04 steps = 172, shift = 16.7, angle = 11.9 degrees Position of cryosparc_P4_J288_map_locres_forJ285 z flip (#38) relative to CS_P4_J285_sharp_flip.mrc (#32) coordinates: Matrix rotation and translation -0.15731459 0.96448973 -0.21215945 50.76791567 -0.83839054 -0.24396591 -0.48742375 323.17714111 -0.52187488 0.10119361 0.84699849 86.68679965 Axis 0.30630695 0.16117090 -0.93818974 Axis point 169.99659509 146.99779714 0.00000000 Rotation angle (degrees) 106.08964492 Shift along axis -13.69134858 > ui mousemode right ""translate selected models"" > view matrix models > #38,-0.29391,0.88572,-0.35933,106.9,-0.78003,-0.43953,-0.4454,363.34,-0.55243,0.14938,0.82006,93.87 > ui mousemode right ""rotate selected models"" > volume #38 level 4.082 > view matrix models > #38,-0.44764,0.81063,-0.37749,140.89,-0.70715,-0.57929,-0.40543,367.19,-0.54732,0.085454,0.83255,100.3 > ui mousemode right ""translate selected models"" [Repeated 1 time(s)] > view matrix models > #38,-0.44764,0.81063,-0.37749,135.23,-0.70715,-0.57929,-0.40543,367.93,-0.54732,0.085454,0.83255,97.332 > view matrix models > #38,-0.44764,0.81063,-0.37749,134.86,-0.70715,-0.57929,-0.40543,366.07,-0.54732,0.085454,0.83255,96.949 > select subtract #38 Nothing selected > hide #!38 models > color sample #32.1 map #38 palette > 0,#ffb17f:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.286, maximum 42.51 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/CS_P4_J282_sharp_flip.mrc"" Opened CS_P4_J282_sharp_flip.mrc as #39, grid size 320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32 > hide #!32 models > close #39 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J282_005_volume_map_sharp.mrc"" Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J287_map_locres.mrc"" Opened cryosparc_P4_J287_map_locres_forJ282 as #39, grid size 320,320,320, pixel 0.831, shown at level 9.77, step 2, values float32 > volume #39 level 4.139 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J287_map_locres.mrc"" Opened cryosparc_P4_J287_map_locres_forJ282 as #40, grid size 320,320,320, pixel 0.831, shown at level 9.77, step 2, values float32 > close #40 > color sample #35.1 map #39 palette > 0,#ffb17f:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.417, maximum 39.82 > hide #!39 models > volume #35 step 1 > volume #35 level 0.06749 > color sample #35.1 map #39 palette > 0,#ffb17f:1,#527dea:2,#99bfe5:3,#fff6c0:4,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 3.044, mean 3.567, maximum 40.68 > color sample #35.1 map #39 palette > 0,#ffb17f:2,#527dea:3,#99bfe5:4,#fff6c0:5,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 3.044, mean 3.567, maximum 40.68 > color sample #35.1 map #39 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 3.044, mean 3.567, maximum 40.68 > close #32 > close #33 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260503_SA-F_B1_workflow.cxs"" > close #39 > close #38 > close #36 > close #35 > show #!34 models > hide #!34 models > close #34 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J282_005_volume_map_sharp.mrc"" Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J285_006_volume_map_sharp.mrc"" Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0363, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J287_map_locres.mrc"" Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 9.77, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J288_map_locres.mrc"" Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 8.93, step 2, values float32 > rename #37 Color key id #36 Expected a keyword > rename #37 Color_key id #36 Cannot change id of 2D overlay models (Color_key #37) > hide #!33 models > hide #!35 models > volume #34 level 6.298 > volume #34 level 3.171 > volume #34 level 3.779 > hide #!34 models > ui tool show ""Surface Color"" No surface chosen for coloring > show #!34 models > hide #!34 models > color sample #32.1 map #34 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.417, maximum 39.82 > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" Could not find palette custom at COLOURlovers.com using keyword search > show #37 models > key pos 0.558738,0.385722 size 0.0255738,0.0868715 > key pos 0.723062,0.0751149 > key pos 0.862303,0.0795068 > key pos 0.846838,0.0779833 > select add #37 1 model selected > key pos 0.819995,0.0796645 > key pos 0.812107,0.0767711 > key pos 0.825223,0.13099 > select subtract #37 Nothing selected > undo [Repeated 3 time(s)] > color sample #32.1 map #34 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.417, maximum 39.82 > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > show #37 models > select add #37 1 model selected > view matrix models > #37,0.70959,0.62592,0.32358,0.61324,-0.29635,0.68175,-0.66888,-0.0021786,-0.63926,0.37874,0.66925,0.69431 > close #37 > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > hide #!32 models > show #!32 models > volume #32 level 0.04587 > volume #32 level 0.04884 > key pos 0.437353,0.539212 size 0.000454748,0.0481037 > hide #36 models > show #36 models > close #36 > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > ui mousemode right translate > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true [Repeated 1 time(s)] > ui mousemode right ""color key"" > ui mousemode right translate > ui mousemode middle 'color key' > key border false > key border true > key borderWidth 1.0 > key borderWidth 0.0 > key borderWidth 1.0 > key colorTreatment distinct > key colorTreatment blended > ui mousemode middle translate > ui mousemode middle ""color key"" > key borderColor #bfbfbf > key borderColor default > key borderColor #bfbfbf > key borderColor #030303 > key borderColor #020202 > key borderColor #010202 > key borderColor black > key labelColor #bfbfbf > key labelColor default > key fontSize 23 > key fontSize 22 > key fontSize 21 > key fontSize 20 > key fontSize 21 > key fontSize 22 > key fontSize 23 > key fontSize 24 > key bold true > key italic true > key italic false > key numericLabelSpacing equal > key numericLabelSpacing proportional > key labelSide left/top > key labelSide right/bottom > key justification left > key labelSide right/bottom > key justification decimal > key justification right > key justification left > key labelOffset 1.0 > key labelOffset 2.0 > key labelOffset 3.0 > key labelOffset 4.0 > key labelOffset 5.0 > key labelOffset 4.0 > key labelOffset 3.0 > key labelOffset 2.0 > key ticks true > key ticks false > key size 0.26000,0.05000 > key size 0.27000,0.05000 > key size 0.26000,0.05000 > key size 0.25000,0.05000 > key size 0.24000,0.05000 > key size 0.23000,0.05000 > key size 0.22000,0.05000 > key size 0.22000,0.04000 > key size 0.21000,0.04000 > key size 0.20000,0.04000 > key size 0.19000,0.04000 > key bold false > key borderWidth 2.0 > key border false > key border true > key size 0.18000,0.04000 > key size 0.17000,0.04000 > key size 0.17000,0.03000 > key size 0.17000,0.02000 > key size 0.16000,0.02000 > key size 0.15000,0.02000 > key size 0.14000,0.02000 > key size 0.15000,0.02000 > key size 0.14000,0.02000 > key size 0.14000,0.01000 > key size 0.14000,0.02000 > key size 0.14000,0.01000 > key size 0.14000,0.02000 > key size 0.14000,0.03000 > key size 0.14000,0.04000 > key size 0.14000,0.03000 > key bold true > save CS_P4_J282_locres_sharp.png supersample 3 transparentBackground true > hide #!32 models > show #!33 models > show #!35 models > volume #33 level 0.0299 > undo > show #!35 models > volume #35 level 3.774 > hide #!35 models > color sample #33.1 map #35 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.383, maximum 41.2 > volume #33 level 0.03991 > volume #33 level 0.049 > volume #33 level 0.06811 > volume #33 level 0.05628 > volume #33 level 0.05719 > ui mousemode right translate [Repeated 1 time(s)] > select add #37 1 model selected > ui mousemode right translate > select subtract #37 Nothing selected > view #33 > volume #33 level 0.05264 > volume #33 level 0.05082 > save CS_P4_J285_NU_sharp.png supersample 3 transparentBackground true > save CS_P4_J285_locres_sharp.png supersample 3 transparentBackground true > hide #!33 models > show #!32 models > volume #32 level 0.05478 > save CS_P4_J282_locres_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260503_SA-F_B1_workflow1.cxs"" > show #!33 models > hide #!33 models > volume flip #32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > color sample #38.1 map #34 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.643, maximum 46.37 > select add #38 2 models selected > select subtract #38 Nothing selected > show #!34 models > hide #!34 models > show #!32 models > select add #38 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #38,0.96218,0.27239,0.0026401,-33.277,0.27218,-0.96095,-0.049909,243.62,-0.011058,0.04874,-0.99875,256.5 > fitmap #38 inMap #32 Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map cryosparc_P4_J282_005_volume_map_sharp.mrc using 208382 points correlation = 0.3998, correlation about mean = 0.04433, overlap = 423.6 steps = 132, shift = 4.37, angle = 6.4 degrees Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#38) relative to cryosparc_P4_J282_005_volume_map_sharp.mrc (#32) coordinates: Matrix rotation and translation 0.98647244 0.16384860 0.00507628 -21.42824077 0.16385811 -0.98468453 -0.05955579 259.77996198 -0.00475960 0.05958193 -0.99821207 257.16545694 Axis 0.99660933 0.08227896 0.00007951 Axis point 0.00000000 126.91521003 132.48208787 Rotation angle (degrees) 176.57330142 Shift along axis 0.03928788 > select subtract #38 Nothing selected > select add #38 2 models selected > view matrix models > #38,-0.55814,-0.81354,-0.1632,351.46,-0.79796,0.58019,-0.16319,187.27,0.22745,0.039147,-0.973,224.57 > ui mousemode right ""translate selected models"" > view matrix models > #38,-0.55814,-0.81354,-0.1632,337.55,-0.79796,0.58019,-0.16319,184.57,0.22745,0.039147,-0.973,224.6 > fitmap #38 inMap #32 Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map cryosparc_P4_J282_005_volume_map_sharp.mrc using 208382 points correlation = 0.4208, correlation about mean = 0.04628, overlap = 461.9 steps = 76, shift = 2.33, angle = 4.27 degrees Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#38) relative to cryosparc_P4_J282_005_volume_map_sharp.mrc (#32) coordinates: Matrix rotation and translation -0.49732082 -0.85447621 -0.15014131 334.86076124 -0.83743504 0.51801846 -0.17423960 201.03033487 0.22665956 0.03908062 -0.97318968 225.34606158 Axis 0.49228130 -0.86954734 0.03932608 Axis point 210.12674218 0.00000000 138.36301119 Rotation angle (degrees) 167.48677512 Shift along axis -1.09772430 > select subtract #38 Nothing selected > select add #38 2 models selected > view matrix models > #38,-0.49732,-0.85448,-0.15014,335.05,-0.83744,0.51802,-0.17424,201.05,0.22666,0.039081,-0.97319,225.03 > ui mousemode right ""rotate selected models"" > view matrix models > #38,-0.016367,0.99633,0.084023,-21.562,0.99914,0.013095,0.039355,-10.502,0.03811,0.084595,-0.99569,247.71 > ui mousemode right ""translate selected models"" > view matrix models > #38,-0.016367,0.99633,0.084023,-11.414,0.99914,0.013095,0.039355,-8.4507,0.03811,0.084595,-0.99569,248.91 > fitmap #38 inMap #32 Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map cryosparc_P4_J282_005_volume_map_sharp.mrc using 208382 points correlation = 0.4638, correlation about mean = 0.04825, overlap = 549.2 steps = 212, shift = 3.48, angle = 14 degrees Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#38) relative to cryosparc_P4_J282_005_volume_map_sharp.mrc (#32) coordinates: Matrix rotation and translation -0.11733678 0.98529275 -0.12421864 36.78201449 0.98526620 0.13117004 0.10974943 -32.51895072 0.12442908 -0.10951079 -0.98616672 260.89985464 Axis -0.66139292 -0.75003960 -0.00008010 Axis point 18.21387939 0.00000000 132.49954907 Rotation angle (degrees) 170.45882216 Shift along axis 0.04223943 > select subtract #38 Nothing selected > hide #!32 models > color sample #38.1 map #34 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 3.043, mean 3.992, maximum 41.6 > show #!34 models > volume flip #34 Opened cryosparc_P4_J287_map_locres.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > select add #39 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #39,0.92903,0.36038,-0.083822,-29.473,0.36808,-0.92323,0.1103,201.34,-0.037639,-0.13332,-0.99036,275.09 > show #!34 models > fitmap #39 imapt #34 Expected a keyword > fitmap #39 inMap #34 Fit map cryosparc_P4_J287_map_locres.mrc z flip in map cryosparc_P4_J287_map_locres.mrc using 2056381 points correlation = 0.8371, correlation about mean = 0.04941, overlap = 1.057e+08 steps = 612, shift = 15.2, angle = 38.8 degrees Position of cryosparc_P4_J287_map_locres.mrc z flip (#39) relative to cryosparc_P4_J287_map_locres.mrc (#34) coordinates: Matrix rotation and translation 0.49975558 0.86379414 -0.06406286 -38.69544656 0.86380943 -0.49157793 0.11038297 66.86486459 0.06385627 -0.11050260 -0.99182234 270.06743869 Axis -0.86536171 -0.50114779 0.00005993 Axis point 0.00000000 54.63554700 132.55703766 Rotation angle (degrees) 172.66756182 Shift along axis -0.00743630 > select subtract #39 Nothing selected > hide #!39 models > show #!39 models > select add #39 2 models selected > hide #37 models > hide #!38 models > view matrix models > #39,0.37237,-0.92808,0.0029165,218.26,-0.92659,-0.37195,-0.055474,318.12,0.052569,0.017955,-0.99846,254.69 > ui mousemode right ""translate selected models"" > view matrix models > #39,0.37237,-0.92808,0.0029165,208.8,-0.92659,-0.37195,-0.055474,313.9,0.052569,0.017955,-0.99846,255.36 > ui mousemode right ""rotate selected models"" > view matrix models > #39,0.66947,-0.74091,0.05349,135.56,-0.73453,-0.67101,-0.10103,334.54,0.11074,0.028346,-0.99344,245.27 > ui mousemode right ""translate selected models"" > view matrix models > #39,0.66947,-0.74091,0.05349,211.58,-0.73453,-0.67101,-0.10103,368.3,0.11074,0.028346,-0.99344,245.76 > view matrix models > #39,0.66947,-0.74091,0.05349,241.5,-0.73453,-0.67101,-0.10103,381.69,0.11074,0.028346,-0.99344,243.08 > view matrix models > #39,0.66947,-0.74091,0.05349,287.43,-0.73453,-0.67101,-0.10103,402.31,0.11074,0.028346,-0.99344,237.25 > ui mousemode right ""rotate selected models"" > view matrix models > #39,-0.41494,0.89077,-0.18535,241.42,0.8738,0.44692,0.19168,-11.043,0.25358,-0.082424,-0.9638,229.13 > view matrix models > #39,0.99948,-0.019992,0.025148,145.79,-0.021975,-0.99645,0.081215,326.06,0.023435,-0.081726,-0.99638,264.88 > ui mousemode right ""translate selected models"" > view matrix models > #39,0.99948,-0.019992,0.025148,-4.0949,-0.021975,-0.99645,0.081215,259.26,0.023435,-0.081726,-0.99638,270.42 > select subtract #39 Nothing selected > hide #!34 models > color sample #38.1 map #34 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 3.043, mean 3.992, maximum 41.6 > hide #!39 models > show #!38 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J282_005_volume_map_sharp.mrc"" Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #40, grid size 320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32 > hide #!38 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J287_map_locres.mrc"" Opened cryosparc_P4_J287_map_locres.mrc as #41, grid size 320,320,320, pixel 0.831, shown at level 9.77, step 2, values float32 > volume flip #40 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #42, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #41 Opened cryosparc_P4_J287_map_locres.mrc z flip as #43, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume #43 level 4.042 > color sample #42.1 map #43 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.484, maximum 42.57 > hide #!43 models > hide #!42 models > show #!38 models > show #!39 models > show #!40 models > show #!41 models > show #!42 models > show #!43 models > close #43 > close #38 > close #42 > close #41 > close #40 > close #39 > close #37 > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > hide #36 models > volume flip #32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #34 Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #33 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #35 Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > hide #!39 models > hide #!40 models > hide #!38 models > color sample #37.1 map #38 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.731, maximum 41.43 > hide #!37 models > show #!37 models > hide #!37 models > show #!39 models > color sample #39.1 map #40 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.67, maximum 40.73 > volume #39 level 0.05082 > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > show #36 models > select add #36 1 model selected > key pos 0.366468,0.16715 > key pos 0.360149,0.168599 > key labelColor #bfbfbf > key labelColor default > key labelColor #bfbfbf > key labelColor white > key labelColor default > key ticks true > key tickLength 8.0 > key tickThickness 3.0 > key tickThickness 2.0 > key tickThickness 1.0 > key tickLength 10.0 > key tickLength 8.0 > key tickThickness 2.0 > key tickThickness 1.0 > key tickThickness 0.0 > key tickThickness 1.0 > key tickThickness 2.0 > key ticks false > key labelOffset -1.0 > key labelOffset -2.0 > key labelOffset -1.0 > key labelOffset 0.0 > key labelOffset 1.0 > key labelOffset 2.0 > key labelOffset 3.0 > key labelOffset 4.0 > view matrix models #36,1,0,0,-0.86321,0,1,0,-0.41592,0,0,1,0.9887 > select subtract #36 Nothing selected > select add #36 1 model selected > view matrix models #36,1,0,0,-99.598,0,1,0,-41.849,0,0,1,63.569 > view matrix models #36,1,0,0,-99.715,0,1,0,-41.895,0,0,1,63.621 > view matrix models #36,1,0,0,-102.61,0,1,0,-42.915,0,0,1,63.831 > view matrix models #36,1,0,0,-126.49,0,1,0,-56.195,0,0,1,105.79 > view matrix models #36,1,0,0,-152.42,0,1,0,-56.013,0,0,1,31.21 > view matrix models #36,1,0,0,-131.29,0,1,0,-47.985,0,0,1,24.738 > view matrix models #36,1,0,0,-121.36,0,1,0,-44.649,0,0,1,25.261 > view matrix models #36,1,0,0,-121.37,0,1,0,-44.69,0,0,1,25.567 > view matrix models #36,1,0,0,-123.18,0,1,0,-45.336,0,0,1,25.776 > close #36 > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > key pos 0.377773,0.195303 > key pos 0.377554,0.185959 > key borderWidth 3.0 > key labelOffset 1.0 > key labelOffset 2.0 > key labelOffset 3.0 > key labelOffset 4.0 > key labelOffset 5.0 > key labelOffset 6.0 > key size 0.24000,0.05000 > key size 0.23000,0.05000 > key size 0.23000,0.04000 > key size 0.23000,0.03000 > key size 0.22000,0.03000 > key size 0.21000,0.03000 > key size 0.20000,0.03000 > key size 0.19000,0.03000 > key size 0.18000,0.03000 > key size 0.17000,0.03000 > key size 0.16000,0.03000 > key size 0.15000,0.03000 > key size 0.16000,0.03000 > key size 0.17000,0.03000 > key size 0.17000,0.04000 > key size 0.17000,0.05000 > key size 0.17000,0.04000 > key pos 0.36134,0.205524 size 0.0323267,0.199875 > key pos 0.375585,0.243532 size 0.000780577,0.00120384 > key pos 0.393081,0.282969 size 0,0 [Repeated 1 time(s)] > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > hide #!39 models > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > key pos 0.654167,0.35194 size 0.0389145,0.208023 > show #!39 models > key pos 0.434243,0.168612 size 0.0379186,0.161115 > hide #41 models > ui mousemode right ""translate selected models"" > ui mousemode right translate [Repeated 1 time(s)] > select add #41 1 model selected > select subtract #41 Nothing selected > show #41 models > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right select > select clear > ui mousemode right rotate > ui mousemode right translate > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true [Repeated 1 time(s)] > ui mousemode right zoom > ui mousemode right ""translate selected models"" > ui mousemode right select > select clear > select add #41 1 model selected > select clear Drag select of 39 cryosparc_P4_J285_006_volume_map_sharp.mrc z flip > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > select clear Drag select of 39 cryosparc_P4_J285_006_volume_map_sharp.mrc z flip > ui mousemode right translate > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > select subtract #41 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right rotate > ui mousemode right translate > hide #!39 models > show #!39 models > ui mousemode right select > select #39 2 models selected > ui mousemode right rotate > ui mousemode right translate > select subtract #39 Nothing selected > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > hide #!39 models > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode left ""color key"" > ui mousemode left rotate > ui mousemode right 'color key' > key pos 0.683937,0.290603 size 0.0366198,0.178803 > show #!39 models > key pos 0.885363,0.663755 size 0.0185522,0.00687018 > ui mousemode right translate > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > key pos 0.768821,0.24433 size 0.0347996,0.266198 > key labelOffset 7.0 > key labelOffset 8.0 > key labelOffset 9.0 > hide #!39 models > show #!37 models > volume #37 level 0.06504 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260503_SA-F_B1_workflow2.cxs"" > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > key fontSize 25 > key fontSize 26 > key fontSize 27 > key fontSize 28 > key fontSize 29 > key fontSize 30 > key fontSize 31 > key fontSize 32 > key fontSize 33 > key fontSize 34 > key fontSize 35 > save CS_P4_J282_locres_sharp.png supersample 3 transparentBackground true > hide #!37 models > show #!39 models > volume #39 level 0.06897 > volume #39 level 0.06638 > save CS_P4_J285_locres_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260503_SA-F_B1_workflow2.cxs"" > hide #!39 models > hide #41 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/CS_P4_J282_sharp_flip.mrc"" Opened CS_P4_J282_sharp_flip.mrc as #42, grid size 320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe University/19. Model Building/2. AcrF > Project/2. Bound-form/SA-F_B1/Model/aligned_model_for_J282.pdb"" Chain information for aligned_model_for_J282.pdb #43 --- Chain | Description A B C | No description available > hide #!42 models > select #43/BC Nothing selected > select #43/B, C 15672 atoms, 15966 bonds, 2068 residues, 1 model selected > delete sel > show #!42 models > volume zone #42 nearAtoms #43/A > color #43 #FFF6C0 > volume zone #42 nearAtoms #43/A distance 5 Expected a keyword > color zone #42 near #43/A distance 5 > color zone #42 near #43/A distance 5 tran 50 Expected a keyword > color zone #42 near #43/A distance 5 tran 50 Expected a keyword > color #43 #FFF6C0 > color zone #42 near #43/A distance 5 > color #43 #FFF6C0 transparency 50 > color zone #42 near #43/A distance 5 > graphics silhouettes false > lighting full > lighting flat [Repeated 1 time(s)] > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft [Repeated 1 time(s)] > lighting simple > graphics silhouettes false > color #42 #99bfe580 models > hide #43 models > transparency #42 50 > lighting soft > volume #42 level 0.0232 > lighting soft > close #42 > close #43 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J242_class_02_00122_volume_sharp.mrc"" Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #36, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J242_class_01_00122_volume_sharp.mrc"" Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size 128,128,128, pixel 2.08, shown at level 0.178, step 1, values float32 > close #36 > show #!9 models > select add #42 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #42,0.026241,-0.92593,0.37678,198.52,-0.063177,0.37462,0.92502,-34.721,-0.99766,-0.048078,-0.048667,279.22 > ui mousemode right ""translate selected models"" > view matrix models > #42,0.026241,-0.92593,0.37678,198.7,-0.063177,0.37462,0.92502,-33.267,-0.99766,-0.048078,-0.048667,263 > fitmap #42 inMap #9 Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc using 20960 points correlation = 1, correlation about mean = 1, overlap = 1571 steps = 128, shift = 5.08, angle = 27.9 degrees Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#42) relative to cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.99999999 -0.00010909 0.00000609 0.02020954 0.00010909 0.99999995 0.00031305 -0.06272325 -0.00000612 -0.00031305 0.99999995 0.03217050 Axis -0.94414385 0.01842055 0.32901836 Axis point 0.00000000 112.87704178 199.81299213 Rotation angle (degrees) 0.01899762 Shift along axis -0.00965143 > select subtract #42 Nothing selected > select add #42 2 models selected > fitmap #42 inMap #9 Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc using 20960 points correlation = 1, correlation about mean = 1, overlap = 1571 steps = 40, shift = 0.00318, angle = 0.00769 degrees Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#42) relative to cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.99999999 -0.00011772 0.00012933 0.00283694 0.00011769 0.99999996 0.00026066 -0.05912201 -0.00012937 -0.00026064 0.99999996 0.04294746 Axis -0.83040251 0.41209275 0.37498166 Axis point 0.00000000 180.01203882 210.06369623 Rotation angle (degrees) 0.01798432 Shift along axis -0.01061505 > select subtract #42 Nothing selected > hide #!9 models > volume #42 level 0.2579 > color #42 #ffffb2ff models > color #42 #ffffb280 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/CS_P4_J282_sharp_flip.mrc"" Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32 > volume #42 level 0.1954 > select add #42 2 models selected > view matrix models > #42,0.15189,-0.98482,-0.084022,248.42,-0.056394,-0.093504,0.99402,24.018,-0.98679,-0.14625,-0.069741,273.86 > volume #42 level 0.2537 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J169_class_03_00182_volume_sharp.mrc"" Opened cryosparc_P4_J169_class_03_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 > close #43 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J169_class_02_00182_volume_sharp.mrc"" Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.216, step 1, values float32 > select add #43 4 models selected > view matrix models > #42,0.15189,-0.98482,-0.084022,246.73,-0.056394,-0.093504,0.99402,-45.124,-0.98679,-0.14625,-0.069741,235.92,#43,1,0,0,-1.6882,0,1,0,-69.141,0,0,1,-37.947 > view matrix models > #42,0.15189,-0.98482,-0.084022,237,-0.056394,-0.093504,0.99402,126.12,-0.98679,-0.14625,-0.069741,312.08,#43,1,0,0,-11.419,0,1,0,102.11,0,0,1,38.221 > select subtract #42 2 models selected > view matrix models #43,1,0,0,-10.922,0,1,0,105.75,0,0,1,25.23 > ui mousemode right ""rotate selected models"" > view matrix models > #43,0.053361,-0.96815,-0.24461,270.41,-0.10024,-0.24891,0.96332,141.36,-0.99353,-0.026885,-0.11033,315.47 > ui mousemode right ""translate selected models"" > view matrix models > #43,0.053361,-0.96815,-0.24461,276.43,-0.10024,-0.24891,0.96332,50.344,-0.99353,-0.026885,-0.11033,257.37 > ui mousemode right ""rotate selected models"" > view matrix models > #43,0.25016,-0.91768,-0.30868,252.37,-0.0074281,-0.32063,0.94718,48.872,-0.96818,-0.23465,-0.087026,276.42 > ui mousemode right ""translate selected models"" > view matrix models > #43,0.25016,-0.91768,-0.30868,252.17,-0.0074281,-0.32063,0.94718,49.119,-0.96818,-0.23465,-0.087026,280.28 > view matrix models > #43,0.25016,-0.91768,-0.30868,245.18,-0.0074281,-0.32063,0.94718,41.479,-0.96818,-0.23465,-0.087026,278.46 > view matrix models > #43,0.25016,-0.91768,-0.30868,244.24,-0.0074281,-0.32063,0.94718,46.881,-0.96818,-0.23465,-0.087026,278.05 > select add #42 4 models selected > select subtract #43 2 models selected > view matrix models > #42,0.15189,-0.98482,-0.084022,248.26,-0.056394,-0.093504,0.99402,10.768,-0.98679,-0.14625,-0.069741,272.27 > select subtract #42 Nothing selected > color #36 #99BFE5 > hide #!42 models > select add #43 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #43,0.073784,-0.55439,0.82898,66.918,0.0052521,0.83145,0.55558,-43.45,-0.99726,-0.036639,0.064259,236.72 > ui mousemode right ""translate selected models"" > view matrix models > #43,0.073784,-0.55439,0.82898,82.905,0.0052521,0.83145,0.55558,-39.115,-0.99726,-0.036639,0.064259,236.78 > select subtract #43 Nothing selected > volume #36 level 0.0602 > select add #43 2 models selected > view matrix models > #43,0.073784,-0.55439,0.82898,84.941,0.0052521,0.83145,0.55558,-38.546,-0.99726,-0.036639,0.064259,236.53 > view matrix models > #43,0.073784,-0.55439,0.82898,84.833,0.0052521,0.83145,0.55558,-38.074,-0.99726,-0.036639,0.064259,236.34 > volume #43 level 0.1902 > color #43 #b2b2ff80 models > volume #43 level 0.2283 > select add #40 4 models selected > select subtract #40 2 models selected > select subtract #43 Nothing selected > color #43 #ffffb280 models > color #43 #b2b2ff80 models > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260503_SA-F_B1_workflow3.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_cryosparc_P4_J243_003_volume_map_35_TMD_regions_resampled.mrc"" Opened cryosparc_P4_cryosparc_P4_J243_003_volume_map_35_TMD_regions_resampled.mrc as #44, grid size 80,80,80, pixel 3.32, shown at level 0.324, step 1, values float32 > close #44 > save CS_P4_J282_show_mask_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260503_SA-F_B1_workflow4.cxs"" ——— End of log from Sun May 3 17:29:06 2026 ——— > view name session-start opened ChimeraX session > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J295_006_volume_map_sharp.mrc"" Opened cryosparc_P4_J295_006_volume_map_sharp.mrc as #44, grid size 320,320,320, pixel 0.831, shown at level 0.0361, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J296_map_locres.mrc"" Opened cryosparc_P4_J296_map_locres.mrc as #45, grid size 320,320,320, pixel 0.831, shown at level 8.66, step 2, values float32 > hide #!43 models > hide #!36 models > hide #!45 models > show #!45 models > hide #!45 models > volume flip #44 Opened cryosparc_P4_J295_006_volume_map_sharp.mrc z flip as #46, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #45 Opened cryosparc_P4_J296_map_locres.mrc z flip as #47, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #45 > close #44 > rename #46 CS_P4_J295_sharp_flip id #44 > save CS_P4_J295_sharp_flip.mrc #44 > rename #47 CS_P4_J296_locres_flip id #45 > save CS_P4_J296_locres_flip.mrc #45 > ui tool show ""Surface Color"" > hide #!45 models > color sample #44.1 map #45 palette #ffb17f:#527dea:#99bfe5:#fff6c0:#f4fff3 > outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.132, maximum 48.35 > show #41 models > volume #44 level 0.0515 > color sample #44.1 map #45 palette > 1,#ffb17f:2,#527dea:3,#99bfe5:4,#fff6c0:5,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#ffb17f:3,#527dea:4,#ffb17f:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#527dea:3,#99bfe5:4,#ffb17f:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > key #527dea:2 #99bfe5:3 #ffb17f:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#527dea outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > key #f4fff3:2 #fff6c0:3 #ffb17f:4 #99bfe5:5 #527dea:6 showTool true > ui mousemode right ""color key"" > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#527dd6 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#46a2de outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#4d8fde outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#94aec1 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#a78bc1 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#c1a77f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#89b3c1 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > color sample #44.1 map #45 palette > 2,#ffb17f:3,#2c98ee:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#ffb17f:3,#4979d3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > save CS_P4_J295_locres_sharp.png supersample 3 transparentBackground true Cell requested for row 0 is out of bounds for table with 6 rows! Resizing table model. > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260505_SA-F_B1_workflow.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J300_005_volume_map_sharp.mrc"" Opened cryosparc_P4_J300_005_volume_map_sharp.mrc as #46, grid size 320,320,320, pixel 0.831, shown at level 0.0375, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J301_map_locres.mrc"" Opened cryosparc_P4_J301_map_locres.mrc as #47, grid size 320,320,320, pixel 0.831, shown at level 9.68, step 2, values float32 > hide #!44 models > hide #!47 models > volume flip #46 Opened cryosparc_P4_J300_005_volume_map_sharp.mrc z flip as #48, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #47 Opened cryosparc_P4_J301_map_locres.mrc z flip as #49, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #46 > close #47 > rename #48 CS_P4_J300_sharp_flip id #46 > rename #49 CS_P4_J301_locres_flip id #47 > save CS_P4_J301_locres_flip.mrc #47 > save CS_P4_J300_sharp_flip.mrc #46 > color sample #46.1 map #47 palette > 2,#ffb17f:3,#4979d3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.498, maximum 44.88 > hide #!47 models > volume #46 level 0.03399 > volume #46 level 0.06962 > volume #46 level 0.05919 > save CS_P4_J300_locres_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260505_SA-F_B1_workflow.cxs"" ——— End of log from Tue May 5 09:31:57 2026 ——— > view name session-start opened ChimeraX session > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J302_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J302_002_volume_map_sharp.mrc as #48, grid size 80,80,80, pixel 3.32, shown at level 0.658, step 1, values float32 > select add #48 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #48,0.064602,0.97911,0.19278,-26.266,0.98732,-0.034646,-0.1549,22.036,-0.14498,0.20034,-0.96894,229.94 > volume flip #48 Opened cryosparc_P4_J302_002_volume_map_sharp.mrc z flip as #49, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #48 > rename #49 rename > rename #49 CS_P4_J302_sharp_flip id #48 > save CS_P4_J302_sharp_flip.mrc #48 > select add #48 2 models selected > view matrix models > #48,-0.56486,-0.82475,0.026783,324.58,0.77395,-0.54076,-0.32951,143.72,0.28625,-0.1654,0.94377,-52.222 > hide #41 models > hide #!46 models > show #!47 models > hide #!47 models > show #!45 models > hide #!45 models > show #!43 models > hide #!43 models > show #!39 models > ui mousemode right ""translate selected models"" > view matrix models > #48,-0.56486,-0.82475,0.026783,319.51,0.77395,-0.54076,-0.32951,139.04,0.28625,-0.1654,0.94377,-3.8614 > view matrix models > #48,-0.56486,-0.82475,0.026783,321.32,0.77395,-0.54076,-0.32951,140.03,0.28625,-0.1654,0.94377,-10.821 > fitmap $48 inmap #39 Missing or invalid ""atomsOrMap"" argument: invalid objects specifier > fitmap #48 inMap #39 Fit map CS_P4_J302_sharp_flip.mrc in map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip using 5112 points correlation = 0.3608, correlation about mean = 0.02111, overlap = 103.8 steps = 76, shift = 4.71, angle = 3.71 degrees Position of CS_P4_J302_sharp_flip.mrc (#48) relative to cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#39) coordinates: Matrix rotation and translation -0.54436883 -0.83749052 0.04766738 317.13056079 0.79848148 -0.53475206 -0.27652762 129.04232256 0.25707950 -0.11247150 0.95982304 -11.58663120 Axis 0.09898047 -0.12634523 0.98703584 Axis point 124.28808276 149.04371086 0.00000000 Rotation angle (degrees) 124.03152255 Shift along axis 3.64942894 > ui mousemode right ""rotate selected models"" > view matrix models > #48,-0.38435,0.91427,-0.12797,86.018,-0.92117,-0.38898,-0.012326,307,-0.061046,0.11314,0.9917,-2.8083 > fitmap #48 inMap #39 Fit map CS_P4_J302_sharp_flip.mrc in map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip using 5112 points correlation = 0.623, correlation about mean = 0.1973, overlap = 254 steps = 104, shift = 5.55, angle = 8.62 degrees Position of CS_P4_J302_sharp_flip.mrc (#48) relative to cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#39) coordinates: Matrix rotation and translation -0.49090927 0.85957769 -0.14189522 105.36638005 -0.85910240 -0.50468247 -0.08508012 328.20339808 -0.14474501 0.08013591 0.98621858 12.70754555 Axis 0.09568836 0.00165051 -0.99540997 Axis point 147.88121154 133.69042072 0.00000000 Rotation angle (degrees) 120.31054935 Shift along axis -2.02517664 > select subtract #48 Nothing selected > volume #48 level 0.8066 > hide #!48 models > show #!48 models > hide #!39 models > show #!40 models > hide #!40 models > show #!46 models > hide #!46 models > show #!46 models > hide #!46 models > volume #48 level 0.6121 > show #!24 models > hide #!24 models > color #48 #99BFE5 > hide #!48 models > show #!48 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J303_003_volume_map_sharp.mrc"" Opened cryosparc_P4_J303_003_volume_map_sharp.mrc as #49, grid size 80,80,80, pixel 3.32, shown at level 0.57, step 1, values float32 > select add #49 2 models selected > view matrix models > #49,0.53874,0.84077,0.053573,-61.438,0.83514,-0.54134,0.097405,87.116,0.1109,-0.0077344,-0.9938,260.56 > view matrix models > #49,0.53215,0.84494,0.053856,-61.154,0.83957,-0.53484,0.095262,85.896,0.10929,-0.0054773,-0.99399,260.49 > view matrix models > #49,-0.8763,-0.44891,0.17485,296.18,-0.45964,0.88777,-0.024369,82.131,-0.14428,-0.10172,-0.98429,307.41 > volume flip #49 Opened cryosparc_P4_J303_003_volume_map_sharp.mrc z flip as #50, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #49 > rename #50 CS_P4_J303_sharp_flip id #49 > save CS_P4_J303_sharp_flip.mrc #49 > select add #49 2 models selected > view matrix models > #49,-0.44927,0.88595,-0.11509,87.376,-0.86051,-0.46376,-0.21085,349.13,-0.24018,0.0043123,0.97072,61.749 > ui mousemode right ""translate selected models"" > view matrix models > #49,-0.44927,0.88595,-0.11509,93.572,-0.86051,-0.46376,-0.21085,352.06,-0.24018,0.0043123,0.97072,37.843 > fitmap #49 inMap 348 Invalid ""inMap"" argument: invalid density map specifier > fitmap #49 inMap #48 Fit map CS_P4_J303_sharp_flip.mrc in map CS_P4_J302_sharp_flip.mrc using 5118 points correlation = 0.8483, correlation about mean = 0.4386, overlap = 3011 steps = 68, shift = 10.7, angle = 7.19 degrees Position of CS_P4_J303_sharp_flip.mrc (#49) relative to CS_P4_J302_sharp_flip.mrc (#48) coordinates: Matrix rotation and translation 0.99996126 -0.00401528 0.00783497 -1.22617333 0.00399514 0.99998870 0.00258400 -1.26181412 -0.00784526 -0.00255260 0.99996598 1.34185977 Axis -0.28004899 0.85489100 0.43673098 Axis point 178.64594040 0.00000000 162.72002408 Rotation angle (degrees) 0.52546068 Shift along axis -0.14929320 > select subtract #49 Nothing selected > hide #!48 models > color #49 #FCEDFF > hide #!49 models > show #!49 models > volume #49 level 0.5753 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J304_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J304_002_volume_map_sharp.mrc as #50, grid size 80,80,80, pixel 3.32, shown at level 1.66, step 1, values float32 > hide #!49 models > select add #50 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #50,0.25626,0.96633,0.023099,-33.544,0.9662,-0.25539,-0.035012,44.222,-0.027934,0.03129,-0.99912,256.23 > volume #50 level 2.579 > select subtract #50 Nothing selected > volume #50 level 1.975 > volume flip #50 Opened cryosparc_P4_J304_002_volume_map_sharp.mrc z flip as #51, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #50 > rename #51 CS_P4_J304_sharp_flip id #50 > save CS_P4_J304_sharp_flip.mrc #50 > select add #50 2 models selected > show #!49 models > view matrix models > #50,0.25432,0.96619,0.042346,-35.759,0.96711,-0.25431,-0.0057645,40.158,0.0051995,0.042419,-0.99909,250.22 > view matrix models > #50,-0.77557,0.61543,-0.14049,175.22,-0.61485,-0.78688,-0.052719,333.03,-0.143,0.045495,0.98868,11.993 > color #50 #FCEDFF > select subtract #50 Nothing selected > hide #!49 models > hide #!50 models > show #!50 models > volume #50 level 1.954 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J305_003_volume_map_sharp.mrc"" Opened cryosparc_P4_J305_003_volume_map_sharp.mrc as #51, grid size 80,80,80, pixel 3.32, shown at level 0.569, step 1, values float32 > hide #!50 models > select add #51 2 models selected > view matrix models > #51,-0.9391,-0.22026,0.26379,268.58,-0.1463,0.9508,0.27307,-8.1662,-0.31096,0.21785,-0.92512,264.01 > volume flip #51 Opened cryosparc_P4_J305_003_volume_map_sharp.mrc z flip as #52, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #51 > rename #52 CS_P4_J305_sharp_flip id #51 > save CS_P4_J305_sharp_flip.mrc #51 > color #51 #FCEDFF > show #!50 models > select add #51 2 models selected > view matrix models > #51,0.99548,-0.078687,0.053201,5.068,0.073705,0.99322,0.089881,-20.578,-0.059913,-0.085553,0.99453,15.159 > fitmap #51 inMap #50 Fit map CS_P4_J305_sharp_flip.mrc in map CS_P4_J304_sharp_flip.mrc using 5112 points correlation = 0.7769, correlation about mean = 0.3462, overlap = 4325 steps = 92, shift = 6.39, angle = 27.1 degrees Position of CS_P4_J305_sharp_flip.mrc (#51) relative to CS_P4_J304_sharp_flip.mrc (#50) coordinates: Matrix rotation and translation -0.48191930 -0.86211205 -0.15657780 337.25915719 0.86174903 -0.49867166 0.09335524 70.84333299 -0.15856359 -0.08994107 0.98324371 36.25215794 Axis -0.10573285 0.00114549 0.99439391 Axis point 149.95468753 133.49561797 0.00000000 Rotation angle (degrees) 119.91228641 Shift along axis 0.47070508 > select subtract #51 Nothing selected > hide #!50 models > hide #!51 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J306_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J306_002_volume_map_sharp.mrc as #52, grid size 80,80,80, pixel 3.32, shown at level 0.89, step 1, values float32 > select add #52 2 models selected > view matrix models > #52,0.64736,0.71151,-0.27328,-15.881,0.69766,-0.69754,-0.16345,155.65,-0.30692,-0.084848,-0.94795,287.9 > volume flip #52 Opened cryosparc_P4_J306_002_volume_map_sharp.mrc z flip as #53, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #52 > select add #53 2 models selected > show #!51 models > view matrix models > #53,-0.54969,0.82414,-0.13652,114.28,-0.83504,-0.54665,0.062273,314.18,-0.023306,0.14823,0.98868,-59.023 > ui mousemode right ""translate selected models"" > view matrix models > #53,-0.54969,0.82414,-0.13652,112.71,-0.83504,-0.54665,0.062273,313.11,-0.023306,0.14823,0.98868,-22.329 > fitmap #53 inMap #51 Fit map cryosparc_P4_J306_002_volume_map_sharp.mrc z flip in map CS_P4_J305_sharp_flip.mrc using 5118 points correlation = 0.8696, correlation about mean = 0.2872, overlap = 4918 steps = 72, shift = 6.47, angle = 20.6 degrees Position of cryosparc_P4_J306_002_volume_map_sharp.mrc z flip (#53) relative to CS_P4_J305_sharp_flip.mrc (#51) coordinates: Matrix rotation and translation -0.48951817 0.85648171 -0.16374082 109.67271887 -0.85572951 -0.50794021 -0.09860917 331.28158536 -0.16762749 0.09184687 0.98156263 12.77250071 Axis 0.11055185 0.00225605 -0.99386780 Axis point 150.74970822 134.14339059 0.00000000 Rotation angle (degrees) 120.52723515 Shift along axis 0.17773418 > select subtract #53 Nothing selected > hide #!51 models > rename #53 CS_P4_J306_sharp_flip id #52 > save CS_P4_J306_sharp_flip.mrc #52 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J307_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J307_002_volume_map_sharp.mrc as #53, grid size 80,80,80, pixel 3.32, shown at level 0.417, step 1, values float32 > hide #!52 models > select add #53 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #53,-0.97802,-0.15767,0.13647,275.15,-0.15325,0.98728,0.042392,17.478,-0.14141,0.020547,-0.98974,260.92 > volume flip #53 Opened cryosparc_P4_J307_002_volume_map_sharp.mrc z flip as #54, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #53 > select add #54 2 models selected > show #!51 models > view matrix models > #54,-0.83454,0.54308,0.09272,165.84,-0.53719,-0.83947,0.081916,314.21,0.12232,0.018554,0.99232,-51.868 > ui mousemode right ""translate selected models"" > view matrix models > #54,-0.83454,0.54308,0.09272,166.01,-0.53719,-0.83947,0.081916,312.6,0.12232,0.018554,0.99232,-21.112 > fitmap #54 inMap #51 Fit map cryosparc_P4_J307_002_volume_map_sharp.mrc z flip in map CS_P4_J305_sharp_flip.mrc using 5118 points correlation = 0.9157, correlation about mean = 0.3086, overlap = 1346 steps = 92, shift = 8.03, angle = 16.7 degrees Position of cryosparc_P4_J307_002_volume_map_sharp.mrc z flip (#54) relative to CS_P4_J305_sharp_flip.mrc (#51) coordinates: Matrix rotation and translation -0.49196091 0.85478647 -0.16527113 110.59805296 -0.85414546 -0.51062861 -0.09845785 330.98838770 -0.16855261 0.09272817 0.98132130 13.11747971 Axis 0.11118076 0.00190829 -0.99379837 Axis point 150.81392912 133.83273648 0.00000000 Rotation angle (degrees) 120.70607669 Shift along axis -0.10813355 > select subtract #54 Nothing selected > rename #54 CS_P4_J307_sharp_flip id #53 > save CS_P4_J307_sharp_flip.mrc #53 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J308_003_volume_map_sharp.mrc"" Opened cryosparc_P4_J308_003_volume_map_sharp.mrc as #54, grid size 80,80,80, pixel 3.32, shown at level 0.487, step 1, values float32 > hide #!51 models > hide #!53 models > select add #54 2 models selected > view matrix models #54,1,0,0,-2.2085,0,1,0,5.106,0,0,1,17.329 > ui mousemode right ""rotate selected models"" > view matrix models > #54,-0.97907,-0.098429,0.17813,263.99,-0.078474,0.99017,0.11581,3.2524,-0.18778,0.099408,-0.97717,270.12 > volume flip #54 Opened cryosparc_P4_J308_003_volume_map_sharp.mrc z flip as #55, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #54 > select add #55 2 models selected > show #!53 models > view matrix models > #55,-0.032009,-0.99944,0.0094019,279.03,0.99475,-0.030941,0.097574,-4.0943,-0.097229,0.012476,0.99518,-8.8511 > ui mousemode right ""translate selected models"" > view matrix models > #55,-0.032009,-0.99944,0.0094019,275.5,0.99475,-0.030941,0.097574,4.3503,-0.097229,0.012476,0.99518,10.879 > fitmap #55 inMap #53 Fit map cryosparc_P4_J308_003_volume_map_sharp.mrc z flip in map CS_P4_J307_sharp_flip.mrc using 5116 points correlation = 0.9635, correlation about mean = 0.3444, overlap = 1309 steps = 80, shift = 11, angle = 8.02 degrees Position of cryosparc_P4_J308_003_volume_map_sharp.mrc z flip (#55) relative to CS_P4_J307_sharp_flip.mrc (#53) coordinates: Matrix rotation and translation -0.47079667 0.87008681 -0.14594324 102.09450866 -0.87101131 -0.48471046 -0.07996914 326.37268834 -0.14032031 0.08946901 0.98605553 9.07494900 Axis 0.09685875 -0.00321433 -0.99529295 Axis point 148.07793015 132.95152312 0.00000000 Rotation angle (degrees) 118.99450917 Shift along axis -0.19255539 > select subtract #55 Nothing selected > hide #!53 models > color #55 #fcedffff models > rename #55 CS_P4_J308_sharp_flip id #54 > save CS_P4_J308_sharp_flip.mrc #54 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J309_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J309_002_volume_map_sharp.mrc as #55, grid size 80,80,80, pixel 3.32, shown at level 0.427, step 1, values float32 > hide #!54 models > select add #55 2 models selected > show #!54 models > ui mousemode right ""rotate selected models"" > view matrix models > #55,0.72482,-0.68817,-0.032661,133.9,-0.68882,-0.72298,-0.053201,331.74,0.012998,0.061058,-0.99805,234.36 > hide #!54 models > view matrix models > #55,-0.98503,0.14104,0.099091,242.98,0.14443,0.98912,0.027904,-21.89,-0.094078,0.041798,-0.99469,251.29 > volume flip #55 Opened cryosparc_P4_J309_002_volume_map_sharp.mrc z flip as #56, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #55 > select add #56 2 models selected > show #!54 models > view matrix models > #56,-0.63923,0.76709,0.054278,117.91,-0.76391,-0.64153,0.069883,315.42,0.088428,0.0032076,0.99608,-48.086 > ui mousemode right ""translate selected models"" > view matrix models > #56,-0.63923,0.76709,0.054278,118.17,-0.76391,-0.64153,0.069883,313.6,0.088428,0.0032076,0.99608,-18.356 > fitmap #56 inMap #54 Fit map cryosparc_P4_J309_002_volume_map_sharp.mrc z flip in map CS_P4_J308_sharp_flip.mrc using 5111 points correlation = 0.9585, correlation about mean = 0.3571, overlap = 1283 steps = 104, shift = 10.8, angle = 17.1 degrees Position of cryosparc_P4_J309_002_volume_map_sharp.mrc z flip (#56) relative to CS_P4_J308_sharp_flip.mrc (#54) coordinates: Matrix rotation and translation -0.48831434 -0.86312376 -0.12871093 333.56502617 0.86459679 -0.49852007 0.06285020 75.43057430 -0.11841248 -0.08059241 0.98968852 28.18171624 Axis -0.08273806 -0.00594017 0.99655362 Axis point 146.06051902 134.60897835 0.00000000 Rotation angle (degrees) 119.90563147 Shift along axis 0.03799683 > select subtract #56 Nothing selected > hide #!54 models > hide #!56 models > show #!56 models > color #56 #fcedffff models > rename #56 CS_P4_J309_sharp_flip id #55 > save CS_P4_J309_sharp_flip.mrc #55 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J310_003_volume_map_sharp.mrc"" Opened cryosparc_P4_J310_003_volume_map_sharp.mrc as #56, grid size 80,80,80, pixel 3.32, shown at level 0.683, step 1, values float32 > volume flip #56 Opened cryosparc_P4_J310_003_volume_map_sharp.mrc z flip as #57, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #56 > fitmap #56 inMap #52 No atoms or maps for #56 > fitmap #57 inMap #52 Fit map cryosparc_P4_J310_003_volume_map_sharp.mrc z flip in map CS_P4_J306_sharp_flip.mrc using 5115 points correlation = 0.769, correlation about mean = 0.3701, overlap = 4288 steps = 88, shift = 5.42, angle = 22.7 degrees Position of cryosparc_P4_J310_003_volume_map_sharp.mrc z flip (#57) relative to CS_P4_J306_sharp_flip.mrc (#52) coordinates: Matrix rotation and translation -0.48166864 -0.85899522 -0.17355843 339.66736714 0.86194402 -0.50013127 0.08319372 72.72621082 -0.15826501 -0.10952585 0.98130335 38.95738038 Axis -0.11128512 -0.00883113 0.99374928 Axis point 150.89500052 135.18260516 0.00000000 Rotation angle (degrees) 120.01642768 Shift along axis 0.27169032 > hide #!55 models > show #!52 models > color #57 #fcedffff models > hide #!52 models > save #57 CS_P4_J310_sharp_flip id #56 Cannot determine format for '#57' > rename #57 CS_P4_J310_sharp_flip id #56 > save CS_P4_J310_sharp_flip.mrc #56 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J311_004_volume_map_sharp.mrc"" Opened cryosparc_P4_J311_004_volume_map_sharp.mrc as #57, grid size 80,80,80, pixel 3.32, shown at level 0.525, step 1, values float32 > volume flip #57 Opened cryosparc_P4_J311_004_volume_map_sharp.mrc z flip as #58, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #57 > color #58 #fcedffff models > rename #58 CS_P4_J311_sharp_flip id #57 > save CS_P4_J311_sharp_flip.mrc #57 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260506_SA-F_B1_workflow.cxs"" > view P1 > hide #!57 models > hide #!56 models > show #!47 models > hide #!47 models > show #!48 models > save CS_P4_J302_NU_sharp.png supersample 3 transparentBackground true > hide #!48 models > show #!49 models > save CS_P4_J303_NU_sharp.png supersample 3 transparentBackground true > hide #!49 models > show #!50 models > save CS_P4_J304_NU_sharp.png supersample 3 transparentBackground true > hide #!50 models > show #!51 models > save CS_P4_J305_NU_sharp.png supersample 3 transparentBackground true > hide #!51 models > show #!52 models > volume #52 level 1.034 > save CS_P4_J306_NU_sharp.png supersample 3 transparentBackground true > hide #!52 models > show #!53 models > color #53 #fcedffff models > save CS_P4_J307_NU_sharp.png supersample 3 transparentBackground true > hide #!53 models > show #!54 models > save CS_P4_J308_NU_sharp.png supersample 3 transparentBackground true > hide #!54 models > show #!55 models > save CS_P4_J309_NU_sharp.png supersample 3 transparentBackground true > hide #!55 models > show #!56 models > volume #56 level 0.7192 > save CS_P4_J310_NU_sharp.png supersample 3 transparentBackground true > hide #!56 models > show #!57 models > save CS_P4_J311_NU_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260506_SA-F_B1_workflow.cxs"" ——— End of log from Wed May 6 15:19:28 2026 ——— > view name session-start opened ChimeraX session > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J323_006_volume_map_sharp.mrc"" Opened cryosparc_P4_J323_006_volume_map_sharp.mrc as #58, grid size 320,320,320, pixel 0.831, shown at level 0.0345, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J324_map_locres.mrc"" Opened cryosparc_P4_J324_map_locres.mrc as #59, grid size 320,320,320, pixel 0.831, shown at level 8.89, step 2, values float32 > hide #!57 models > hide #!58 models > show #!58 models > hide #!59 models > show #!59 models > volume flip #58 Opened cryosparc_P4_J323_006_volume_map_sharp.mrc z flip as #60, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #59 Opened cryosparc_P4_J324_map_locres.mrc z flip as #61, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #58 > close #59 > rename #60 CS_P4_J323_sharp_flip #58 Expected a keyword > rename #60 CS_P4_J323_sharp_flip id #58 > save CS_P4_J323_sharp_flip.mrc #58 > rename CS_P4_J324_map_locres_flip id #59 Missing or invalid ""models"" argument: invalid models specifier > rename #61 CS_P4_J324_map_locres_flip id #59 > save CS_P4_J324_map_locres_flip.mrc #59 > hide #!58 models > show #!58 models > hide #!59 models > volume #59 level 9.377 > hide #!59 models > volume #58 level 0.05889 > show #!59 models > volume #59 level 3.695 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow.cxs"" > ui tool show ""Surface Color"" > hide #!58 models > show #!58 models > hide #!59 models > color radial #58.1 palette #ffb17f:#4979d3:#99bfe5:#fff6c0:#f4fff3 > color sample #58.1 map #59 palette > 166.9,#ffb17f:198,#4979d3:229.1,#99bfe5:260.3,#fff6c0:291.4,#f4fff3 > outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.552, maximum 44.59 > color sample #58.1 map #59 palette > 2,#ffb17f:3,#4979d3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.552, maximum 44.59 > show #!59 models > hide #!58 models > hide #!59 models > show #!59 models > show #!58 models > hide #!59 models > show #!59 models > hide #!59 models > volume #58 level 0.0634 > volume #58 level 0.04264 > volume #58 level 0.07693 > volume #58 level 0.06069 > volume #58 level 0.07152 > volume #58 level 0.05889 > volume #58 level 0.05167 > volume #58 level 0.06159 > key #ffb17f:2 #4979d3:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > key pos 0.82265,0.196044 size 0.0692066,0.202924 > ui mousemode right translate > ui mousemode right ""color key"" > key pos 0.802943,0.231339 size 0.039822,0.144632 > key #ffb17f:2 #4979d3:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > key pos 0.836801,0.165731 size 0.0516869,0.238605 > show #41 models > key pos 0.820538,0.190547 size 0.0458442,0.242723 > save CS_P4_J323_sharp_flip.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow1.cxs"" > color sample #58.1 map #59 palette > 2,#ffb17f:3,#169bd3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.532, maximum 44.61 > color sample #58.1 map #59 palette > 2,#ffb17f:3,#46c7f6:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.532, maximum 44.61 > color sample #58.1 map #59 palette > 2,#ffb17f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.532, maximum 44.61 > key #ffb17f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > color sample #58.1 map #59 palette > 2,#ffb17f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.532, maximum 44.61 > key #ffb17f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #ffb17f:6 showTool true > color sample #58.1 map #59 palette > 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.532, maximum 44.61 > key #13097f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #ffb17f:6 showTool true > save CS_P4_J323_sharp_flip2.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow2.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J329_005_volume_map_sharp.mrc"" Opened cryosparc_P4_J329_005_volume_map_sharp.mrc as #60, grid size 320,320,320, pixel 0.831, shown at level 0.0384, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J330_map_locres.mrc"" Opened cryosparc_P4_J330_map_locres.mrc as #61, grid size 320,320,320, pixel 0.831, shown at level 9.71, step 2, values float32 > hide #!58 models > hide #!60 models > show #!60 models > hide #!61 models > volume flip #60 Opened cryosparc_P4_J329_005_volume_map_sharp.mrc z flip as #62, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #61 Opened cryosparc_P4_J330_map_locres.mrc z flip as #63, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #60 > close #61 > rename #62 CS_P4_J329_sharp_flip id #60 > save CS_P4_J329_sharp_flip.mrc #60 > rename #63 rename > rename #63 CS_P4_J330_locres_flip id #61 > save CS_P4_J330_locres_flip.mrc #61 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow3.cxs"" > hide #!61 models > color sample #58.1 map #59 palette > 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.532, maximum 44.61 > color sample #60.1 map #61 palette > 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.466, maximum 46.71 > volume #60 level 0.06443 > key #13097f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #ffb17f:6 showTool true > ui mousemode right ""color key"" > volume #60 level 0.05663 > save CS_P4_J329_locres_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow3.cxs"" ——— End of log from Thu May 7 15:58:17 2026 ——— > view name session-start opened ChimeraX session > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J300_005_volume_map_sharp.mrc"" Opened cryosparc_P4_J300_005_volume_map_sharp.mrc as #62, grid size 320,320,320, pixel 0.831, shown at level 0.0375, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J301_map_locres.mrc"" Opened cryosparc_P4_J301_map_locres.mrc as #63, grid size 320,320,320, pixel 0.831, shown at level 9.68, step 2, values float32 > hide #!60 models > hide #!63 models > volume flip #62 Opened cryosparc_P4_J300_005_volume_map_sharp.mrc z flip as #64, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #63 Opened cryosparc_P4_J301_map_locres.mrc z flip as #65, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #62 > close #63 > rename #64 CS_P4_J300_sharp_flip id #62 > save CS_P4_J300_sharp_flip.mrc #62 > rename #65 CS_P4_J301_locres_flip id #63 > save CS_P4_J301_locres_flip.mrc #63 > show #!46 models > show #!47 models > hide #!47 models > hide #!46 models > hide #!63 models > show #!63 models > volume #63 level 3.952 > hide #!63 models > volume #62 level 0.0392 > ui tool show ""Surface Color"" > color sample #62.1 map #63 palette #13097f:#11b6e1:#99bfe5:#fff6c0:#ffb17f > outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.383, maximum 43.37 > color sample #62.1 map #63 palette > 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.383, maximum 43.37 > show #!63 models > hide #!63 models > hide #!62 models > show #!62 models > volume #62 level 0.06614 > volume #62 level 0.05745 > save CS_P4_J300_locres_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow4.cxs"" > open /Users/peiyuyu/Downloads/cryosparc_P7_J110_004_volume_map_sharp.mrc Opened cryosparc_P7_J110_004_volume_map_sharp.mrc as #64, grid size 160,160,160, pixel 1.66, shown at level 0.28, step 1, values float32 > hide #!62 models > close #64 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow5.cxs"" ——— End of log from Thu May 7 21:11:39 2026 ——— > view name session-start opened ChimeraX session > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J323_006_volume_map_sharp2.mrc"" Opened cryosparc_P4_J323_006_volume_map_sharp2.mrc as #64, grid size 320,320,320, pixel 0.831, shown at level 0.0329, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J324_map_locres2.mrc"" Opened cryosparc_P4_J324_map_locres2.mrc as #65, grid size 320,320,320, pixel 0.831, shown at level 8.98, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J329_006_volume_map_sharp2.mrc"" Opened cryosparc_P4_J329_006_volume_map_sharp2.mrc as #66, grid size 320,320,320, pixel 0.831, shown at level 0.0389, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J330_map_locres2.mrc"" Opened cryosparc_P4_J330_map_locres2.mrc as #67, grid size 320,320,320, pixel 0.831, shown at level 9.65, step 2, values float32 > hide #!66 models > hide #!67 models > hide #!65 models > close #66 > close #67 > volume flip #64 Opened cryosparc_P4_J323_006_volume_map_sharp2.mrc z flip as #66, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #65 Opened cryosparc_P4_J324_map_locres2.mrc z flip as #67, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume #66 level 0.04422 > volume #67 level 3.812 > hide #!66 models > hide #!67 models > show #!67 models > hide #!67 models > show #!66 models > close #64 > close #65 > rename #66 CS_P4_J323_sharp2_flip id #64 > save CS_P4_J323_sharp2_flip.mrc #64 > rename CS_P4_J324_locres2_flip id #65 Missing or invalid ""models"" argument: invalid models specifier > rename CS_P4_J324_locres2_flip id #65 Missing or invalid ""models"" argument: invalid models specifier > rename #67 CS_P4_J324_locres2_flip id #65 > save CS_P4_J324_locres2_flip.mrc #65 > hide #!64 models > show #!65 models > hide #!65 models > show #!64 models > volume #64 level 0.05469 > ui tool show ""Surface Color"" ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow5.cxs"" Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel 2.08, shown at level 0.185, step 1, values float32 Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel 2.08, shown at level 0.356, step 1, values float32 Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown at level 1.17, step 1, values float32 Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size 128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size 128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32 Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size 128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32 Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size 128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32 Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size 128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32 Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size 128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32 Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel 2.08, shown at level 0.335, step 1, values float32 Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size 128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32 Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown at level 1.29, step 1, values float32 Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size 128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32 Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size 128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel 2.08, shown at level 0.271, step 1, values float32 Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size 128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32 Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32, shown at level 1.6, step 1, values float32 Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown at level 0.649, step 1, values float32 Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown at level 1.01, step 1, values float32 Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown at level 0.533, step 1, values float32 Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown at level 0.567, step 1, values float32 Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.134, step 1, values float32 Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.143, step 1, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32 Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 2, values float32 Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 2, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size 320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32 Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 1, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32 Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size 128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32 Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 0.0602, step 2, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32 Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831, shown at level 0.0515, step 1, values float32 Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831, shown at level 8.66, step 1, values float32 Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831, shown at level 0.0592, step 1, values float32 Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831, shown at level 9.68, step 1, values float32 Opened CS_P4_J302_sharp_flip.mrc as #48, grid size 80,80,80, pixel 3.32, shown at level 0.612, step 1, values float32 Opened CS_P4_J303_sharp_flip.mrc as #49, grid size 80,80,80, pixel 3.32, shown at level 0.575, step 1, values float32 Opened CS_P4_J304_sharp_flip.mrc as #50, grid size 80,80,80, pixel 3.32, shown at level 1.95, step 1, values float32 Opened CS_P4_J305_sharp_flip.mrc as #51, grid size 80,80,80, pixel 3.32, shown at level 0.569, step 1, values float32 Opened CS_P4_J306_sharp_flip.mrc as #52, grid size 80,80,80, pixel 3.32, shown at level 1.03, step 1, values float32 Opened CS_P4_J307_sharp_flip.mrc as #53, grid size 80,80,80, pixel 3.32, shown at level 0.417, step 1, values float32 Opened CS_P4_J308_sharp_flip.mrc as #54, grid size 80,80,80, pixel 3.32, shown at level 0.487, step 1, values float32 Opened CS_P4_J309_sharp_flip.mrc as #55, grid size 80,80,80, pixel 3.32, shown at level 0.427, step 1, values float32 Opened CS_P4_J310_sharp_flip.mrc as #56, grid size 80,80,80, pixel 3.32, shown at level 0.719, step 1, values float32 Opened CS_P4_J311_sharp_flip.mrc as #57, grid size 80,80,80, pixel 3.32, shown at level 0.525, step 1, values float32 Opened CS_P4_J323_sharp_flip.mrc as #58, grid size 320,320,320, pixel 0.831, shown at level 0.0616, step 1, values float32 Opened CS_P4_J324_map_locres_flip.mrc as #59, grid size 320,320,320, pixel 0.831, shown at level 3.69, step 1, values float32 Opened CS_P4_J329_sharp_flip.mrc as #60, grid size 320,320,320, pixel 0.831, shown at level 0.0566, step 1, values float32 Opened CS_P4_J330_locres_flip.mrc as #61, grid size 320,320,320, pixel 0.831, shown at level 9.71, step 1, values float32 Opened CS_P4_J300_sharp_flip.mrc as #62, grid size 320,320,320, pixel 0.831, shown at level 0.0575, step 1, values float32 Opened CS_P4_J301_locres_flip.mrc as #63, grid size 320,320,320, pixel 0.831, shown at level 3.95, step 1, values float32 Log from Thu May 7 21:11:39 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow3.cxs"" Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel 2.08, shown at level 0.185, step 1, values float32 Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel 2.08, shown at level 0.356, step 1, values float32 Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown at level 1.17, step 1, values float32 Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size 128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size 128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32 Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size 128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32 Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size 128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32 Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size 128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32 Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size 128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32 Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel 2.08, shown at level 0.335, step 1, values float32 Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size 128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32 Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown at level 1.29, step 1, values float32 Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size 128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32 Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size 128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel 2.08, shown at level 0.271, step 1, values float32 Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size 128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32 Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32, shown at level 1.6, step 1, values float32 Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown at level 0.649, step 1, values float32 Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown at level 1.01, step 1, values float32 Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown at level 0.533, step 1, values float32 Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown at level 0.567, step 1, values float32 Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.134, step 1, values float32 Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.143, step 1, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32 Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 2, values float32 Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 2, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size 320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32 Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 1, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32 Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size 128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32 Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 0.0602, step 2, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32 Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831, shown at level 0.0515, step 1, values float32 Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831, shown at level 8.66, step 1, values float32 Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831, shown at level 0.0592, step 1, values float32 Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831, shown at level 9.68, step 1, values float32 Opened CS_P4_J302_sharp_flip.mrc as #48, grid size 80,80,80, pixel 3.32, shown at level 0.612, step 1, values float32 Opened CS_P4_J303_sharp_flip.mrc as #49, grid size 80,80,80, pixel 3.32, shown at level 0.575, step 1, values float32 Opened CS_P4_J304_sharp_flip.mrc as #50, grid size 80,80,80, pixel 3.32, shown at level 1.95, step 1, values float32 Opened CS_P4_J305_sharp_flip.mrc as #51, grid size 80,80,80, pixel 3.32, shown at level 0.569, step 1, values float32 Opened CS_P4_J306_sharp_flip.mrc as #52, grid size 80,80,80, pixel 3.32, shown at level 1.03, step 1, values float32 Opened CS_P4_J307_sharp_flip.mrc as #53, grid size 80,80,80, pixel 3.32, shown at level 0.417, step 1, values float32 Opened CS_P4_J308_sharp_flip.mrc as #54, grid size 80,80,80, pixel 3.32, shown at level 0.487, step 1, values float32 Opened CS_P4_J309_sharp_flip.mrc as #55, grid size 80,80,80, pixel 3.32, shown at level 0.427, step 1, values float32 Opened CS_P4_J310_sharp_flip.mrc as #56, grid size 80,80,80, pixel 3.32, shown at level 0.719, step 1, values float32 Opened CS_P4_J311_sharp_flip.mrc as #57, grid size 80,80,80, pixel 3.32, shown at level 0.525, step 1, values float32 Opened CS_P4_J323_sharp_flip.mrc as #58, grid size 320,320,320, pixel 0.831, shown at level 0.0616, step 1, values float32 Opened CS_P4_J324_map_locres_flip.mrc as #59, grid size 320,320,320, pixel 0.831, shown at level 3.69, step 1, values float32 Opened CS_P4_J329_sharp_flip.mrc as #60, grid size 320,320,320, pixel 0.831, shown at level 0.0566, step 1, values float32 Opened CS_P4_J330_locres_flip.mrc as #61, grid size 320,320,320, pixel 0.831, shown at level 9.71, step 1, values float32 Log from Thu May 7 15:58:17 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260506_SA-F_B1_workflow.cxs"" Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel 2.08, shown at level 0.185, step 1, values float32 Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel 2.08, shown at level 0.356, step 1, values float32 Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown at level 1.17, step 1, values float32 Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size 128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size 128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32 Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size 128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32 Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size 128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32 Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size 128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32 Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size 128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32 Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel 2.08, shown at level 0.335, step 1, values float32 Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size 128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32 Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown at level 1.29, step 1, values float32 Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size 128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32 Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size 128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel 2.08, shown at level 0.271, step 1, values float32 Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size 128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32 Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32, shown at level 1.6, step 1, values float32 Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown at level 0.649, step 1, values float32 Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown at level 1.01, step 1, values float32 Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown at level 0.533, step 1, values float32 Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown at level 0.567, step 1, values float32 Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.134, step 1, values float32 Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.143, step 1, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32 Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 2, values float32 Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 2, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size 320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32 Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 1, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32 Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size 128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32 Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 0.0602, step 2, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32 Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831, shown at level 0.0515, step 1, values float32 Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831, shown at level 8.66, step 1, values float32 Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831, shown at level 0.0592, step 1, values float32 Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831, shown at level 9.68, step 1, values float32 Opened CS_P4_J302_sharp_flip.mrc as #48, grid size 80,80,80, pixel 3.32, shown at level 0.612, step 1, values float32 Opened CS_P4_J303_sharp_flip.mrc as #49, grid size 80,80,80, pixel 3.32, shown at level 0.575, step 1, values float32 Opened CS_P4_J304_sharp_flip.mrc as #50, grid size 80,80,80, pixel 3.32, shown at level 1.95, step 1, values float32 Opened CS_P4_J305_sharp_flip.mrc as #51, grid size 80,80,80, pixel 3.32, shown at level 0.569, step 1, values float32 Opened CS_P4_J306_sharp_flip.mrc as #52, grid size 80,80,80, pixel 3.32, shown at level 1.03, step 1, values float32 Opened CS_P4_J307_sharp_flip.mrc as #53, grid size 80,80,80, pixel 3.32, shown at level 0.417, step 1, values float32 Opened CS_P4_J308_sharp_flip.mrc as #54, grid size 80,80,80, pixel 3.32, shown at level 0.487, step 1, values float32 Opened CS_P4_J309_sharp_flip.mrc as #55, grid size 80,80,80, pixel 3.32, shown at level 0.427, step 1, values float32 Opened CS_P4_J310_sharp_flip.mrc as #56, grid size 80,80,80, pixel 3.32, shown at level 0.719, step 1, values float32 Opened CS_P4_J311_sharp_flip.mrc as #57, grid size 80,80,80, pixel 3.32, shown at level 0.525, step 1, values float32 Log from Wed May 6 15:19:28 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260505_SA-F_B1_workflow.cxs"" Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel 2.08, shown at level 0.185, step 1, values float32 Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel 2.08, shown at level 0.356, step 1, values float32 Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown at level 1.17, step 1, values float32 Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size 128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size 128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32 Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size 128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32 Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size 128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32 Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size 128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32 Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size 128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32 Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel 2.08, shown at level 0.335, step 1, values float32 Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size 128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32 Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown at level 1.29, step 1, values float32 Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size 128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32 Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size 128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel 2.08, shown at level 0.271, step 1, values float32 Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size 128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32 Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32, shown at level 1.6, step 1, values float32 Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown at level 0.649, step 1, values float32 Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown at level 1.01, step 1, values float32 Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown at level 0.533, step 1, values float32 Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown at level 0.567, step 1, values float32 Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.134, step 1, values float32 Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.143, step 1, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32 Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 2, values float32 Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 2, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size 320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32 Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 1, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32 Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size 128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32 Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 0.0602, step 2, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32 Opened CS_P4_J295_sharp_flip.mrc as #44, grid size 320,320,320, pixel 0.831, shown at level 0.0515, step 1, values float32 Opened CS_P4_J296_locres_flip.mrc as #45, grid size 320,320,320, pixel 0.831, shown at level 8.66, step 1, values float32 Opened CS_P4_J300_sharp_flip.mrc as #46, grid size 320,320,320, pixel 0.831, shown at level 0.0592, step 1, values float32 Opened CS_P4_J301_locres_flip.mrc as #47, grid size 320,320,320, pixel 0.831, shown at level 9.68, step 1, values float32 Log from Tue May 5 09:31:57 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260503_SA-F_B1_workflow4.cxs"" Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J216_class_0_sharp_flip.mrc as #1, grid size 128,128,128, pixel 2.08, shown at level 0.185, step 1, values float32 Opened CS_P4_J216_class_1_sharp_flip.mrc as #2, grid size 128,128,128, pixel 2.08, shown at level 0.203, step 1, values float32 Opened CS_P4_J216_class_2_sharp_flip.mrc as #3, grid size 128,128,128, pixel 2.08, shown at level 0.356, step 1, values float32 Opened CS_P4_J219_sharp_flip.mrc as #6, grid size 80,80,80, pixel 3.32, shown at level 1.17, step 1, values float32 Opened CS_P4_J244_sharp_flip.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size 128,128,128, pixel 2.08, shown at level 0.221, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size 128,128,128, pixel 2.08, shown at level 0.146, step 1, values float32 Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size 128,128,128, pixel 2.08, shown at level 0.15, step 1, values float32 Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size 128,128,128, pixel 2.08, shown at level 0.345, step 1, values float32 Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size 128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32 Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size 128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32 Opened CS_P4_J117_class_02_sharp_flip.mrc as #15, grid size 128,128,128, pixel 2.08, shown at level 0.335, step 1, values float32 Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size 128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32 Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 Opened CS_P4_J120_sharp_flip.mrc as #18, grid size 80,80,80, pixel 3.32, shown at level 1.29, step 1, values float32 Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size 128,128,128, pixel 2.08, shown at level 0.156, step 1, values float32 Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size 128,128,128, pixel 2.08, shown at level 0.198, step 1, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 Opened CS_P4_J169_class_03_sharp_flip.mrc as #22, grid size 128,128,128, pixel 2.08, shown at level 0.271, step 1, values float32 Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size 128,128,128, pixel 2.08, shown at level 0.2, step 1, values float32 Opened CS_P4_J176_NU_sharp_flip.mrc as #24, grid size 80,80,80, pixel 3.32, shown at level 1.6, step 1, values float32 Opened CS_P4_J255_sharp_flip.mrc as #25, grid size 80,80,80, pixel 3.32, shown at level 0.649, step 1, values float32 Opened CS_P4_J256_sharp_flip.mrc as #26, grid size 80,80,80, pixel 3.32, shown at level 1.01, step 1, values float32 Opened CS_P4_J257_sharp_flip.mrc as #27, grid size 80,80,80, pixel 3.32, shown at level 1.16, step 1, values float32 Opened CS_P4_J258_sharp_flip.mrc as #28, grid size 80,80,80, pixel 3.32, shown at level 0.533, step 1, values float32 Opened CS_P4_J259_sharp_flip.mrc as #29, grid size 80,80,80, pixel 3.32, shown at level 0.567, step 1, values float32 Opened CS_P4_J267_sharp_flip.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.134, step 1, values float32 Opened CS_P4_J277_sharp_flip.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.143, step 1, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0548, step 2, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0508, step 2, values float32 Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 2, values float32 Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 2, values float32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size 320,320,320, pixel 0.831, shown at level 0.065, step 1, values float32 Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at level 3.78, step 1, values float32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at level 0.0664, step 1, values float32 Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320, pixel 0.831, shown at level 3.77, step 1, values float32 Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size 128,128,128, pixel 2.08, shown at level 0.254, step 1, values float32 Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 0.0602, step 2, values float32 Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.228, step 1, values float32 Log from Sun May 3 17:29:06 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J216_class_00_00122_volume_sharp.mrc"" Opened cryosparc_P4_J216_class_00_00122_volume_sharp.mrc as #1, grid size 128,128,128, pixel 2.08, shown at level 0.204, step 1, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J216_class_01_00122_volume_sharp.mrc"" Opened cryosparc_P4_J216_class_01_00122_volume_sharp.mrc as #2, grid size 128,128,128, pixel 2.08, shown at level 0.218, step 1, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J216_class_02_00122_volume_sharp.mrc"" Opened cryosparc_P4_J216_class_02_00122_volume_sharp.mrc as #3, grid size 128,128,128, pixel 2.08, shown at level 0.263, step 1, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J216_class_03_00122_volume_sharp.mrc"" Opened cryosparc_P4_J216_class_03_00122_volume_sharp.mrc as #4, grid size 128,128,128, pixel 2.08, shown at level 0.199, step 1, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J216_class_04_00122_volume_sharp.mrc"" Opened cryosparc_P4_J216_class_04_00122_volume_sharp.mrc as #5, grid size 128,128,128, pixel 2.08, shown at level 0.235, step 1, values float32 > lighting soft > set bgColor white > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!5 models > hide #!5 models > show #!4 models > volume #4 level 0.2842 > show #!3 models > hide #!4 models > volume #3 level 0.3546 > volume #3 level 0.356 > hide #!3 models > show #!1 models > show #!2 models > hide #!2 models > show #!5 models > hide #!1 models > color #1 #FCEDFF > hide #!5 models > show #!1 models > show #!2 models > hide #!1 models > show #!3 models > hide #!3 models > show #!3 models > hide #!2 models > show #!4 models > hide #!3 models > hide #!4 models > show #!5 models > hide #!5 models > show #!1 models > volume flip #1 Opened cryosparc_P4_J216_class_00_00122_volume_sharp.mrc z flip as #6, grid size 128,128,128, pixel 2.08, shown at step 1, values float32 > hide #!6 models > show #!2 models > volume flip #2 Opened cryosparc_P4_J216_class_01_00122_volume_sharp.mrc z flip as #7, grid size 128,128,128, pixel 2.08, shown at step 1, values float32 > hide #!7 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > volume flip #3 Opened cryosparc_P4_J216_class_02_00122_volume_sharp.mrc z flip as #8, grid size 128,128,128, pixel 2.08, shown at step 1, values float32 > show #!4 models > hide #!4 models > show #!5 models > hide #!8 models > hide #!5 models > close #1 > close #2 > close #3 > rename #6 CS_P4_J216_class_0_sharp_flip id #1 > save #1 CS_P4_J216_class_0_sharp_flip.mrc Cannot determine format for '#1' > save CS_P4_J216_class_0_sharp_flip.mrc #1 > rename #7 CS_P4_J216_class_1_sharp_flip id #1_sharp_flip.mrc #2 Invalid ""id"" argument: Expected an integer > rename #7 CS_P4_J216_class_1_sharp_flip id #1_sharp_flip id #2 Invalid ""id"" argument: Expected an integer > rename #7 CS_P4_J216_class_2_sharp_flip id #2 > rename #2 CS_P4_J216_class_1_sharp_flip > rename #8 CS_P4_J216_class_2_sharp_flip id #3 > save CS_P4_J216_class_1_sharp_flip.mrc #2 > save CS_P4_J216_class_2_sharp_flip.mrc #3 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260430_SA-F_B1_workflow.cxs"" > show #!1 models > show #!2 models > show #!3 models > show #!4 models > show #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!3 models > hide #!3 models > show #!4 models > hide #!5 models > hide #!4 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!5 models > show #!3 models > hide #!5 models > show #!1 models > select add #1 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,-2.4868,0,1,0,6.8233,0,0,1,22.302 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.85834,-0.51214,-0.03115,83.967,-0.50924,-0.85776,0.070198,298.29,-0.06267,-0.044391,-0.99705,270.86 Must specify one map, got 0 > fitmap #1 inMap #3 Fit map CS_P4_J216_class_0_sharp_flip.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 20952 points correlation = 0.8163, correlation about mean = 0.111, overlap = 1135 steps = 116, shift = 13.1, angle = 14.8 degrees Position of CS_P4_J216_class_0_sharp_flip.mrc (#1) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation 0.94377261 -0.32509802 0.06003771 31.40521096 -0.32212557 -0.94514622 -0.05416389 308.66342237 0.07435299 0.03177871 -0.99672551 251.62777867 Axis 0.98583616 -0.16420866 0.03409658 Axis point 0.00000000 154.16030965 128.66405805 Rotation angle (degrees) 177.50176084 Shift along axis -11.14516800 > select subtract #1 Nothing selected > hide #!3 models > hide #!1 models > show #!2 models > show #!3 models > fitmap #2 inMap #3 Fit map CS_P4_J216_class_1_sharp_flip.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 20964 points correlation = 0.8775, correlation about mean = 0.2387, overlap = 1535 steps = 72, shift = 7.04, angle = 9.35 degrees Position of CS_P4_J216_class_1_sharp_flip.mrc (#2) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation 0.99017956 0.04949629 -0.13074615 12.42570756 -0.06022022 0.99502365 -0.07938169 18.18421737 0.12616642 0.08647569 0.98823276 -19.36289944 Axis 0.51051058 -0.79077932 -0.33770846 Axis point 165.72686650 0.00000000 88.43510724 Rotation angle (degrees) 9.34870453 Shift along axis -1.49723285 > hide #!2 models > show #!4 models > fitmap #4 inMap #3 Fit map cryosparc_P4_J216_class_03_00122_volume_sharp.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 5887 points correlation = 0.7186, correlation about mean = 0.04573, overlap = 331.9 steps = 104, shift = 11.1, angle = 13.1 degrees Position of cryosparc_P4_J216_class_03_00122_volume_sharp.mrc (#4) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation 0.97455290 -0.13512397 0.17885231 -1.53434267 0.14053006 0.98991548 -0.01785084 -17.74958210 -0.17463660 0.04253071 0.98371398 30.92421506 Axis 0.13349556 0.78151692 0.60943437 Axis point 157.21397711 0.00000000 34.50744362 Rotation angle (degrees) 13.07084305 Shift along axis 4.76985279 > hide #!4 models > show #!5 models > select add #5 2 models selected > view matrix models > #5,0.70232,-0.70945,-0.058532,142.48,-0.70661,-0.70474,0.063551,312.49,-0.086337,-0.0032735,-0.99626,292.78 > fitmap #5 inMap #3 Fit map cryosparc_P4_J216_class_04_00122_volume_sharp.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 20952 points correlation = 0.896, correlation about mean = 0.3255, overlap = 1903 steps = 100, shift = 4.43, angle = 13 degrees Position of cryosparc_P4_J216_class_04_00122_volume_sharp.mrc (#5) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation 0.72688934 -0.68457986 0.05461051 119.19907428 -0.67457364 -0.72664609 -0.13013783 337.91149541 0.12877226 0.05775699 -0.98999082 252.38058253 Axis 0.92902840 -0.36668580 0.04947481 Axis point 0.00000000 185.59312596 132.22855036 Rotation angle (degrees) 174.19607958 Shift along axis -0.68154259 > select subtract #5 Nothing selected > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260430_SA-F_B1_workflow.cxs"" > hide #!5 models > show #!5 models > hide #!3 models > show #!1 models > hide #!5 models > hide #!1 models > show #!2 models > color #2 #FCEDFF > hide #!2 models > show #!4 models > color #4 #FCEDFF > hide #!4 models > show #!5 models > color #5 #FCEDFF > hide #!5 models > show #!3 models > color #5 #E9C29B > color #5 #FCEDFF > color #3 #E9C29B > ui mousemode right translate > volume #2 level 0.356 > volume #1 level 0.356 > volume #4 level 0.356 > volume #5 level 0.356 > hide #!3 models > show #!1 models > undo [Repeated 1 time(s)] > hide #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #1 level 0.1727 > volume #1 level 0.1851 > show #!2 models > hide #!1 models > volume #2 level 0.203 > show #!3 models > hide #!2 models > hide #!3 models > show #!4 models > volume #4 level 0.1532 > show #!3 models > select add #4 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #4,0.97455,-0.13512,0.17885,1.3208,0.14053,0.98992,-0.017851,-10.868,-0.17464,0.042531,0.98371,31.337 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.085498,-0.64922,0.75578,120.23,0.99605,-0.074063,0.049058,8.8958,0.024125,0.75698,0.65299,-39.323 > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.085498,-0.64922,0.75578,134.23,0.99605,-0.074063,0.049058,6.1939,0.024125,0.75698,0.65299,-87.477 > view matrix models > #4,-0.085498,-0.64922,0.75578,134.33,0.99605,-0.074063,0.049058,6.22,0.024125,0.75698,0.65299,-87.742 > view matrix models > #4,-0.085498,-0.64922,0.75578,130.4,0.99605,-0.074063,0.049058,5.0583,0.024125,0.75698,0.65299,-76.883 > fitmap #4 inMap #3 Fit map cryosparc_P4_J216_class_03_00122_volume_sharp.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 42435 points correlation = 0.7796, correlation about mean = 0.1614, overlap = 1558 steps = 228, shift = 2.07, angle = 23.4 degrees Position of cryosparc_P4_J216_class_03_00122_volume_sharp.mrc (#4) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation -0.31733316 -0.35582789 0.87902570 104.58434579 0.93180439 -0.28920783 0.21931579 18.83015631 0.17618244 0.88867618 0.42333722 -81.48445272 Axis 0.41511738 0.43588247 0.79855121 Axis point 65.64014873 66.59534740 0.00000000 Rotation angle (degrees) 126.27076538 Shift along axis -13.44699307 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.85396,0.083596,-0.51358,313.46,-0.52034,-0.13698,0.8429,94.578,0.00011363,0.98704,0.16047,-34.579 > fitmap #4 inMap #3 Fit map cryosparc_P4_J216_class_03_00122_volume_sharp.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 42435 points correlation = 0.7628, correlation about mean = 0.1138, overlap = 1507 steps = 160, shift = 8.1, angle = 11.6 degrees Position of cryosparc_P4_J216_class_03_00122_volume_sharp.mrc (#4) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation -0.75756109 0.20637267 -0.61928307 295.50473254 -0.63935005 -0.04324082 0.76769900 115.47474727 0.13165378 0.97751755 0.16470194 -51.62941296 Axis 0.18240424 -0.65282152 -0.73522293 Axis point 168.50534676 17.73009752 0.00000000 Rotation angle (degrees) 144.89006320 Shift along axis 16.47604383 > select subtract #4 Nothing selected > volume #4 level 0.3211 > hide #!3 models > volume #4 level 0.2347 > volume #4 level 0.2031 > hide #!4 models > show #!5 models > volume #5 level 0.1924 > volume #5 level 0.2064 > ui mousemode right translate > show #!3 models > hide #!5 models > color #3 #B9DBD5 > hide #!3 models > show #!1 models > lighting shadows true intensity 0.5 > lighting flat > graphics silhouettes false > graphics silhouettes true > lighting soft > save P4_J216_class_0_sharp.png supersample 3 transparentBackground true > hide #!1 models > show #!2 models > save P4_J216_class_1_sharp.png supersample 3 transparentBackground true > hide #!2 models > show #!3 models > save P4_J216_class_2_sharp.png supersample 3 transparentBackground true > hide #!3 models > show #!4 models > save P4_J216_class_3_sharp.png supersample 3 transparentBackground true > hide #!4 models > show #!5 models > show #!1 models > show #!2 models > show #!3 models > show #!4 models > hide #!4 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!1 models > view name P1 [Repeated 1 time(s)] > save P4_J216_class_0_sharp.png supersample 3 transparentBackground true > hide #!1 models > show #!2 models > save P4_J216_class_1_sharp.png supersample 3 transparentBackground true > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!3 models > save P4_J216_class_2_sharp.png supersample 3 transparentBackground true > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!4 models > save P4_J216_class_3_sharp.png supersample 3 transparentBackground true > hide #!4 models > show #!5 models > vieww P1 Unknown command: vieww P1 > view P1 [Repeated 1 time(s)] > save P4_J216_class_4_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260430_SA-F_B1_workflow.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J219_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J219_002_volume_map_sharp.mrc as #6, grid size 80,80,80, pixel 3.32, shown at level 0.854, step 1, values float32 > hide #!5 models > show #!3 models > select add #6 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.50968,-0.8597,0.033732,182.49,-0.85693,-0.50376,0.10903,313.05,-0.076743,-0.084479,-0.99347,263.76 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.50968,-0.8597,0.033732,181.37,-0.85693,-0.50376,0.10903,307.2,-0.076743,-0.084479,-0.99347,286.3 > fitmap #6 inMap #3 Fit map cryosparc_P4_J219_002_volume_map_sharp.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 5120 points correlation = 0.7368, correlation about mean = 0.07448, overlap = 1741 steps = 88, shift = 8.42, angle = 12.4 degrees Position of cryosparc_P4_J219_002_volume_map_sharp.mrc (#6) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation 0.68179907 -0.73031354 0.04233404 134.55628275 -0.72995927 -0.67538450 0.10495351 308.10402853 -0.04805721 -0.10245933 -0.99357566 283.32032359 Axis -0.91672636 0.39951261 0.00156579 Axis point 0.00000000 192.14085888 132.24148806 Rotation angle (degrees) 173.50439997 Shift along axis 0.18377410 > volume #6 level 1.828 > select subtract #6 Nothing selected > hide #!3 models > volume #6 level 1.172 > show #!3 models > select add #6 2 models selected > view matrix models > #6,0.6818,-0.73031,0.042334,145.51,-0.72996,-0.67538,0.10495,294.75,-0.048057,-0.10246,-0.99358,285.84 > view matrix models > #6,0.6818,-0.73031,0.042334,133.79,-0.72996,-0.67538,0.10495,309.04,-0.048057,-0.10246,-0.99358,282.76 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.47143,0.87224,0.13024,-67.58,0.87592,-0.44591,-0.18423,88.863,-0.10262,0.20093,-0.97422,246.36 > fitmap #6 inMap #3 Fit map cryosparc_P4_J219_002_volume_map_sharp.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 3507 points correlation = 0.7523, correlation about mean = 0.053, overlap = 1436 steps = 84, shift = 11, angle = 9.96 degrees Position of cryosparc_P4_J219_002_volume_map_sharp.mrc (#6) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation 0.31271016 0.94213099 0.12083688 -48.05138587 0.94223385 -0.29160641 -0.16480619 65.68302492 -0.12003221 0.16539317 -0.97889599 255.74245569 Axis 0.80789250 0.58932983 0.00025166 Axis point 0.00000000 34.02227920 132.07845223 Rotation angle (degrees) 168.20805262 Shift along axis -0.04702893 > select subtract #6 Nothing selected > hide #!6 models > show #!6 models > select add #6 2 models selected > view matrix models > #6,-0.96774,-0.18791,0.16785,278.55,-0.18769,0.98208,0.017294,25.636,-0.16809,-0.014768,-0.98566,287.91 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.96774,-0.18791,0.16785,272.6,-0.18769,0.98208,0.017294,32.876,-0.16809,-0.014768,-0.98566,284.26 > fitmap #6 inMap #3 Fit map cryosparc_P4_J219_002_volume_map_sharp.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 3507 points correlation = 0.7248, correlation about mean = 0.05418, overlap = 1264 steps = 60, shift = 9.72, angle = 10.6 degrees Position of cryosparc_P4_J219_002_volume_map_sharp.mrc (#6) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation -0.92647017 -0.30027989 0.22690311 266.55888821 -0.26721766 0.94935570 0.16528304 28.41095713 -0.26504293 0.09249729 -0.95978982 282.00607809 Axis -0.14603906 0.98705219 0.06633684 Axis point 153.43261550 0.00000000 122.88099835 Rotation angle (degrees) 165.56984584 Shift along axis 7.82248126 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.92785,-0.005043,0.37292,209.61,0.027742,0.99621,0.082497,-9.3167,-0.37192,0.086891,-0.92419,293.48 > fitmap #6 inMap #3 Fit map cryosparc_P4_J219_002_volume_map_sharp.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 3507 points correlation = 0.7519, correlation about mean = 0.05711, overlap = 1436 steps = 100, shift = 5.47, angle = 14.5 degrees Position of cryosparc_P4_J219_002_volume_map_sharp.mrc (#6) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation -0.92643320 -0.21423055 0.30955905 249.03084383 -0.21368345 0.97623560 0.03610312 27.35482068 -0.30993696 -0.03270052 -0.95019459 303.95121642 Axis -0.11038513 0.99388850 0.00087774 Axis point 150.47041621 0.00000000 131.94319456 Rotation angle (degrees) 161.84114382 Shift along axis -0.03486954 > select subtract #6 Nothing selected > hide #!3 models > hide #!6 models > show #!3 models > hide #!3 models > show #!6 models > volume flip #6 Opened cryosparc_P4_J219_002_volume_map_sharp.mrc z flip as #7, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #6 > rename CS_P4_J219_sharp_flip id #6 Missing or invalid ""models"" argument: invalid models specifier > rename #7 CS_P4_J219_sharp_flip id #6 > save CS_P4_J219_sharp_flip.mrc #6 > show #!3 models > select add #6 2 models selected > view matrix models > #6,0.55385,-0.83087,-0.054,184.1,0.82508,0.55638,-0.098423,-37.993,0.11182,0.009957,0.99368,-50.391 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.55385,-0.83087,-0.054,173.54,0.82508,0.55638,-0.098423,-43.189,0.11182,0.009957,0.99368,-15.893 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.43591,-0.88398,-0.16899,334.46,0.87276,-0.46105,0.1604,51.515,-0.2197,-0.077569,0.97248,45.011 > fitmap #6 inMap #3 Fit map CS_P4_J219_sharp_flip.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 3507 points correlation = 0.9414, correlation about mean = 0.4694, overlap = 2583 steps = 72, shift = 3.53, angle = 4.05 degrees Position of CS_P4_J219_sharp_flip.mrc (#6) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation -0.45821390 -0.85833568 -0.23086770 342.48607306 0.85407817 -0.49711214 0.15306861 63.33623820 -0.24615139 -0.12704090 0.96086946 56.91191433 Axis -0.16142412 0.00880783 0.98684582 Axis point 157.30567711 132.03749632 0.00000000 Rotation angle (degrees) 119.81679395 Shift along axis 1.43562700 > select subtract #6 Nothing selected > hide #!3 models Unsupported scale factor (0.000000) detected on Display1 [Repeated 2 time(s)] > hide #!6 models > show #!3 models > show #!6 models > hide #!6 models > color #3 #B1DCFC > save P4_J216_class_2_sharp.png supersample 3 transparentBackground true > hide #!3 models > show #!3 models > hide #!3 models > show #!6 models > hide #!6 models > show #!3 models > show #!6 models > hide #!3 models > hide #!6 models > show #!3 models > color #3 #AFDBFF > hide #!3 models > show #!6 models > show #!3 models > hide #!3 models > show #!3 models > hide #!6 models > show #!6 models > color #3 #99BFE5 > hide #!6 models > view P1 > save P4_J216_class_2_sharp.png supersample 3 transparentBackground true > hide #!3 models > show #!6 models > ui mousemode right translate > save P4_J219_NU_sharp_flip.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260430_SA-F_B1_workflow.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J243_003_volume_map_sharp.mrc"" Opened cryosparc_P4_J243_003_volume_map_sharp.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.1, step 1, values float32 > select add #7 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.34351,0.88804,0.30558,-69.154,0.93106,-0.36463,0.013018,61.425,0.12299,0.28005,-0.95208,168.53 > view matrix models > #7,-0.72211,0.66266,0.19859,108.59,0.68148,0.73076,0.039546,-55.441,-0.11892,0.16389,-0.97928,217.85 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.72211,0.66266,0.19859,107.8,0.68148,0.73076,0.039546,-63.119,-0.11892,0.16389,-0.97928,255.33 > view matrix models > #7,-0.72211,0.66266,0.19859,116.79,0.68148,0.73076,0.039546,-56.849,-0.11892,0.16389,-0.97928,258.31 > fitmap #7 inMap #6 Fit map cryosparc_P4_J243_003_volume_map_sharp.mrc in map CS_P4_J219_sharp_flip.mrc using 5116 points correlation = 0.9377, correlation about mean = 0.7097, overlap = 1.519e+04 steps = 76, shift = 2.16, angle = 10.6 degrees Position of cryosparc_P4_J243_003_volume_map_sharp.mrc (#7) relative to CS_P4_J219_sharp_flip.mrc (#6) coordinates: Matrix rotation and translation 0.96909604 0.16642828 0.18208375 -39.18937125 0.15922720 -0.98578684 0.05358170 236.77616183 0.18841328 -0.02293313 -0.98182203 241.04145354 Axis -0.99224103 -0.08208102 -0.09338329 Axis point 0.00000000 122.34870623 120.06626952 Rotation angle (degrees) 177.79032322 Shift along axis -3.05877231 > select subtract #7 Nothing selected > select add #7 2 models selected > view matrix models > #7,-0.62422,0.77517,0.097247,102.65,0.77737,0.62868,-0.021408,-52.876,-0.077732,0.062233,-0.99503,269.09 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.32669,-0.93485,0.13901,287.37,-0.94032,0.30667,-0.14745,222.88,0.095218,-0.17888,-0.97925,277.34 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.32669,-0.93485,0.13901,281.61,-0.94032,0.30667,-0.14745,233.21,0.095218,-0.17888,-0.97925,273.65 > fitmap #7 inMap #6 Fit map cryosparc_P4_J243_003_volume_map_sharp.mrc in map CS_P4_J219_sharp_flip.mrc using 5116 points correlation = 0.9419, correlation about mean = 0.7222, overlap = 1.551e+04 steps = 56, shift = 3.52, angle = 7.25 degrees Position of cryosparc_P4_J243_003_volume_map_sharp.mrc (#7) relative to CS_P4_J219_sharp_flip.mrc (#6) coordinates: Matrix rotation and translation -0.62645631 0.77281267 0.10155321 101.66723571 0.77509514 0.63140454 -0.02357570 -50.90352474 -0.08234076 0.06394425 -0.99455072 266.97848709 Axis 0.42971205 0.90289643 0.01120665 Axis point 70.49413903 0.00000000 130.93970837 Rotation angle (degrees) 174.15511884 Shift along axis 0.71895896 > select subtract #7 Nothing selected > hide #!6 models > volume #7 level 1.41 > color #7 #99BFE5 > view P1 > close #7 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J244_003_volume_map_sharp.mrc"" Opened cryosparc_P4_J244_003_volume_map_sharp.mrc as #7, grid size 80,80,80, pixel 3.32, shown at level 1.05, step 1, values float32 > show #!6 models > select add #7 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.71966,-0.6805,-0.13788,149.49,-0.69285,-0.71678,-0.078638,342.79,-0.045318,0.15212,-0.98732,223.99 > hide #!6 models > show #!6 models > ui mousemode right ""translate selected models"" > view matrix models > #7,0.71966,-0.6805,-0.13788,149.4,-0.69285,-0.71678,-0.078638,338.98,-0.045318,0.15212,-0.98732,258.19 > select subtract #7 Nothing selected > hide #!6 models > volume flip #7 Opened cryosparc_P4_J244_003_volume_map_sharp.mrc z flip as #8, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #7 > rename #8 CS_P4_J244_sharp_flip id #7 > save CS_P4_J244_sharp_flip.mrc #7 > color #7 #99BFE5 > volume #7 level 1.156 > save CS_P4_J244_sharp_flip.mrc #7 > save P4_J244_NU_sharp_flip.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J242_class_00_00122_volume_sharp.mrc"" Opened cryosparc_P4_J242_class_00_00122_volume_sharp.mrc as #8, grid size 128,128,128, pixel 2.08, shown at level 0.192, step 1, values float32 > hide #!7 models > volume #8 level 0.2208 > show #!7 models > select add #8 2 models selected > view matrix models #8,1,0,0,1.7912,0,1,0,4.218,0,0,1,1.8536 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.019063,-0.87425,-0.4851,301.31,0.055421,0.48537,-0.87255,194.56,0.99828,-0.010251,0.057705,27.748 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.019063,-0.87425,-0.4851,303.09,0.055421,0.48537,-0.87255,199.03,0.99828,-0.010251,0.057705,19.845 > view matrix models > #8,0.019063,-0.87425,-0.4851,323.73,0.055421,0.48537,-0.87255,193.31,0.99828,-0.010251,0.057705,17.439 > view matrix models > #8,0.019063,-0.87425,-0.4851,322.89,0.055421,0.48537,-0.87255,188.18,0.99828,-0.010251,0.057705,19.28 > fitmap #8 inMap #7 Fit map cryosparc_P4_J242_class_00_00122_volume_sharp.mrc in map CS_P4_J244_sharp_flip.mrc using 14754 points correlation = 0.481, correlation about mean = 0.07756, overlap = 1756 steps = 112, shift = 13.3, angle = 15.3 degrees Position of cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) relative to CS_P4_J244_sharp_flip.mrc (#7) coordinates: Matrix rotation and translation 0.05423844 -0.87969653 0.47243223 170.87663448 0.10002936 0.47553549 0.87399092 -59.90285646 -0.99350507 -0.00014682 0.11378778 232.31099922 Axis -0.44417982 0.74489379 0.49783284 Axis point 199.16697689 -0.00000000 41.59458970 Rotation angle (degrees) 100.26604714 Shift along axis -4.86917491 > select subtract #8 Nothing selected > hide #!7 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J242_class_01_00122_volume_sharp.mrc"" Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #9, grid size 128,128,128, pixel 2.08, shown at level 0.178, step 1, values float32 > hide #!8 models > volume #9 level 0.1464 > show #!8 models > select add #9 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.01099,0.99675,0.079835,4.9565,0.1314,-0.080587,0.98805,-14.68,0.99127,-0.00036851,-0.13186,9.8 > ui mousemode right ""translate selected models"" > view matrix models > #9,0.01099,0.99675,0.079835,10.903,0.1314,-0.080587,0.98805,5.6709,0.99127,-0.00036851,-0.13186,51.786 > view matrix models > #9,0.01099,0.99675,0.079835,4.7224,0.1314,-0.080587,0.98805,-1.1935,0.99127,-0.00036851,-0.13186,45.788 > fitmap #9 inMap #8 Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_00_00122_volume_sharp.mrc using 29766 points correlation = 0.8496, correlation about mean = 0.3082, overlap = 1328 steps = 284, shift = 18.3, angle = 53.9 degrees Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) relative to cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) coordinates: Matrix rotation and translation 0.99575722 -0.02668322 0.08806571 -8.52134797 -0.09034177 -0.46538978 0.88048323 89.22150736 0.01749075 -0.88470354 -0.46582584 307.69453028 Axis -0.99855360 0.03992375 -0.03601119 Axis point 0.00000000 137.23273941 127.10917488 Rotation angle (degrees) 117.88699495 Shift along axis 0.99063260 > select subtract #9 Nothing selected > hide #!8 models > hide #!9 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J242_class_02_00122_volume_sharp.mrc"" Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #10, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 > select add #10 2 models selected > show #!9 models > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.17462,0.93232,0.31669,19.869,0.21917,0.35036,-0.91061,163.76,-0.95993,-0.089597,-0.26552,316.03 > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.17462,0.93232,0.31669,8.7975,0.21917,0.35036,-0.91061,193.69,-0.95993,-0.089597,-0.26552,324.3 > view matrix models > #10,-0.17462,0.93232,0.31669,5.0809,0.21917,0.35036,-0.91061,186.44,-0.95993,-0.089597,-0.26552,324.52 > fitmap #10 inMap #9 Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc using 20970 points correlation = 0.8182, correlation about mean = 0.3079, overlap = 1048 steps = 212, shift = 18, angle = 29.3 degrees Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative to cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) coordinates: Matrix rotation and translation -0.92160797 -0.37293352 0.10751436 286.70013052 -0.37621404 0.79028143 -0.48365097 141.61699812 0.09540306 -0.48618500 -0.86863249 299.79876520 Axis -0.19795503 0.94611818 -0.25626978 Axis point 158.67244900 0.00000000 168.59386356 Rotation angle (degrees) 179.63327476 Shift along axis 0.40332117 > select subtract #10 Nothing selected > hide #!9 models > hide #!10 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J242_class_03_00122_volume_sharp.mrc"" Opened cryosparc_P4_J242_class_03_00122_volume_sharp.mrc as #11, grid size 128,128,128, pixel 2.08, shown at level 0.218, step 1, values float32 > volume #11 level 0.1502 > show #!10 models > select add #11 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #11,0.73904,-0.47164,0.48101,26.135,-0.11204,0.61802,0.77814,-47.481,-0.66427,-0.62897,0.4039,253.49 > ui mousemode right ""translate selected models"" > view matrix models > #11,0.73904,-0.47164,0.48101,5.5926,-0.11204,0.61802,0.77814,-27.642,-0.66427,-0.62897,0.4039,266.06 > ui mousemode right ""rotate selected models"" > view matrix models > #11,-0.56676,0.0073102,0.82385,78.335,0.19153,-0.97139,0.14038,216.5,0.80131,0.23736,0.54915,-63.542 > select subtract #11 Nothing selected > fitmap #11 inMap #10 Fit map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 45754 points correlation = 0.7333, correlation about mean = -0.04196, overlap = 1268 steps = 132, shift = 23.8, angle = 15.3 degrees Position of cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) relative to cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates: Matrix rotation and translation -0.26691235 0.13508665 -0.95420616 300.80664915 -0.90776913 -0.36770197 0.20186745 274.07355373 -0.32359389 0.92007981 0.22077169 18.93443182 Axis 0.50771970 -0.44579332 -0.73721708 Axis point 236.02557416 49.14154001 0.00000000 Rotation angle (degrees) 134.98497404 Shift along axis 16.58651491 > hide #!10 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J242_class_04_00122_volume_sharp.mrc"" Opened cryosparc_P4_J242_class_04_00122_volume_sharp.mrc as #12, grid size 128,128,128, pixel 2.08, shown at level 0.261, step 1, values float32 > show #!10 models > hide #!10 models > select add #12 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #12,1,0,0,-3.7479,0,1,0,3.9168,0,0,1,20.991 > ui mousemode right ""rotate selected models"" > view matrix models > #12,0.79132,-0.13023,0.59737,-27.645,0.22144,0.97176,-0.081485,-12.263,-0.56989,0.19676,0.79781,93.603 > ui mousemode right ""translate selected models"" > view matrix models > #12,0.79132,-0.13023,0.59737,-50.124,0.22144,0.97176,-0.081485,3.5285,-0.56989,0.19676,0.79781,102.68 > view matrix models > #12,0.79132,-0.13023,0.59737,-48.335,0.22144,0.97176,-0.081485,2.277,-0.56989,0.19676,0.79781,101.98 > view matrix models > #12,0.79132,-0.13023,0.59737,-41.566,0.22144,0.97176,-0.081485,-1.9637,-0.56989,0.19676,0.79781,101.41 > fitmap #12 inMap #11 Fit map cryosparc_P4_J242_class_04_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc using 20956 points correlation = 0.8514, correlation about mean = 0.04285, overlap = 1430 steps = 80, shift = 7.16, angle = 11.7 degrees Position of cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) relative to cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) coordinates: Matrix rotation and translation -0.93263188 0.26201641 0.24808299 197.07280134 -0.29117819 -0.95255879 -0.08858337 308.05329962 0.21310334 -0.15485204 0.96468016 17.95641726 Axis -0.11870856 0.06265985 -0.99095006 Axis point 119.69175871 140.62215054 0.00000000 Rotation angle (degrees) 163.79210928 Shift along axis -21.88556717 > select subtract #12 Nothing selected > hide #!11 models > volume #12 level 0.4033 > volume #12 level 0.3453 > color #8 #FCEDFF > hide #!12 models > show #!8 models > hide #!8 models > show #!9 models > color #9 #FCEDFF > hide #!9 models > show #!10 models > color #10 #FCEDFF > hide #!10 models > show #!11 models > color #11 #FCEDFF > hide #!11 models > show #!12 models > color #12 #99BFE5 > view P1 > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!1 models > hide #!1 models > show #!6 models > hide #!6 models > show #!3 models > select add #12 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #12,0.95369,-0.29732,-0.045496,35.025,0.29889,0.95373,0.032695,-17.906,0.03367,-0.044779,0.99843,26.075 > view matrix models > #12,-0.8879,0.32078,-0.32974,233.6,0.30063,0.94715,0.1119,-26.299,0.34821,0.00022498,-0.93742,198.42 > ui mousemode right ""translate selected models"" > view matrix models > #12,-0.8879,0.32078,-0.32974,232.89,0.30063,0.94715,0.1119,-34.317,0.34821,0.00022498,-0.93742,213.72 > view matrix models > #12,-0.8879,0.32078,-0.32974,243.25,0.30063,0.94715,0.1119,-55.273,0.34821,0.00022498,-0.93742,214.76 > ui mousemode right ""rotate selected models"" > view matrix models > #12,-0.88731,0.39919,0.23093,169.34,0.40717,0.91324,-0.014156,-50.796,-0.21654,0.081466,-0.97287,283.71 > fitmap #12 inMap #3 Fit map cryosparc_P4_J242_class_04_00122_volume_sharp.mrc in map CS_P4_J216_class_2_sharp_flip.mrc using 12546 points correlation = 0.9893, correlation about mean = 0.7632, overlap = 2433 steps = 124, shift = 11, angle = 27.9 degrees Position of cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) relative to CS_P4_J216_class_2_sharp_flip.mrc (#3) coordinates: Matrix rotation and translation -0.62359754 0.77535022 0.09979057 101.14085164 0.77719680 0.62864768 -0.02769904 -50.42984630 -0.08420957 0.06028386 -0.99462285 268.88184712 Axis 0.43136931 0.90213001 0.00905357 Axis point 70.24601107 0.00000000 131.83510298 Rotation angle (degrees) 174.14674629 Shift along axis 0.56912319 > select subtract #12 Nothing selected > hide #!12 models > show #!12 models > show #!11 models > select add #11 2 models selected > view matrix models > #11,-0.37852,0.89247,0.24538,28.817,0.88041,0.42898,-0.20213,16.101,-0.28566,0.13952,-0.94812,300.03 > ui mousemode right ""translate selected models"" > view matrix models > #11,-0.37852,0.89247,0.24538,46.8,0.88041,0.42898,-0.20213,-5.6117,-0.28566,0.13952,-0.94812,300.85 > view matrix models > #11,-0.37852,0.89247,0.24538,36.63,0.88041,0.42898,-0.20213,-16.953,-0.28566,0.13952,-0.94812,296.6 > fitmap #11 inMap #12 Fit map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_04_00122_volume_sharp.mrc using 45754 points correlation = 0.7192, correlation about mean = 0.1299, overlap = 1714 steps = 96, shift = 6.98, angle = 12.7 degrees Position of cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) relative to cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.88557701 -0.25567312 -0.38779454 99.27082409 0.32552043 0.93717068 0.12548928 -53.44589150 0.33134544 -0.23736546 0.91316364 -22.95393091 Axis -0.36530839 -0.72400286 0.58512361 Axis point 106.02252826 0.00000000 214.34257569 Rotation angle (degrees) 29.77806268 Shift along axis -11.00037360 > select subtract #11 Nothing selected > hide #!12 models > show #!12 models > hide #!12 models > hide #!3 models > show #!12 models > hide #!11 models > show #!10 models > select add #10 2 models selected > view matrix models > #10,-0.49822,0.81176,0.30466,37.524,-0.14214,0.27015,-0.95227,247.33,-0.85532,-0.51775,-0.019207,343.36 > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.013344,0.85199,0.52339,-68.961,-0.1627,-0.51831,0.83957,128.11,0.98659,-0.073951,0.14553,-15.381 > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.013344,0.85199,0.52339,-45.161,-0.1627,-0.51831,0.83957,119.13,0.98659,-0.073951,0.14553,-13.578 > fitmap #10 inMap #12 Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_04_00122_volume_sharp.mrc using 20970 points correlation = 0.7101, correlation about mean = 0.02358, overlap = 908.6 steps = 80, shift = 7.98, angle = 9.33 degrees Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative to cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.35385865 -0.88893073 0.29083707 267.80089120 -0.02210060 0.31881642 0.94755878 -31.84809054 -0.93503776 0.32887420 -0.13246184 232.75133151 Axis -0.38099533 0.75491227 0.53380711 Axis point 205.22642342 0.00000000 36.94010088 Rotation angle (degrees) 125.71487620 Shift along axis -1.82908632 > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.12287,-0.47662,0.87048,95.543,0.19038,-0.87215,-0.45067,269.26,0.97399,0.11035,0.1979,-37.789 > select subtract #10 Nothing selected > hide #!12 models > show #!11 models > show #!12 models > hide #!10 models > hide #!12 models > show #!10 models > select add #10 2 models selected > view matrix models > #10,-0.38685,-0.21971,0.89558,99.669,-0.053858,-0.96416,-0.2598,294.54,0.92057,-0.14874,0.36115,-16.709 > fitmap #10 inMap #11 Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc using 20970 points correlation = 0.8482, correlation about mean = 0.1221, overlap = 870.1 steps = 88, shift = 3.31, angle = 12.5 degrees Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative to cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) coordinates: Matrix rotation and translation -0.32110732 -0.67353914 -0.66575904 357.49560201 0.09667773 -0.72262784 0.68444314 122.97291760 -0.94209527 0.15541563 0.29715733 219.46626263 Axis -0.54292343 0.28359472 0.79044809 Axis point 234.55310205 82.20310947 0.00000000 Rotation angle (degrees) 150.84311237 Shift along axis 14.25842210 > view matrix models > #10,-0.30509,0.38504,-0.87101,233.77,0.18733,0.92101,0.34153,-54.422,0.93372,-0.058973,-0.35312,61.617 > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.30509,0.38504,-0.87101,240.35,0.18733,0.92101,0.34153,-58.712,0.93372,-0.058973,-0.35312,49.559 > view matrix models > #10,-0.30509,0.38504,-0.87101,238.16,0.18733,0.92101,0.34153,-58.03,0.93372,-0.058973,-0.35312,51.895 > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.36524,0.52001,-0.77213,217.65,0.08187,0.84416,0.5298,-55.56,0.9273,0.13029,-0.3509,28.264 > fitmap #10 inMap #11 Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc using 20970 points correlation = 0.8485, correlation about mean = 0.1929, overlap = 854.7 steps = 140, shift = 18.2, angle = 22.5 degrees Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative to cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) coordinates: Matrix rotation and translation -0.33967352 0.22689098 0.91276633 25.87088295 0.00914596 0.97121791 -0.23801704 28.63290177 -0.94049893 -0.07249996 -0.33197214 335.97765353 Axis 0.08835402 0.98928424 -0.11623361 Axis point 129.11230783 0.00000000 160.33867701 Rotation angle (degrees) 110.50039702 Shift along axis -8.44002041 > view matrix models > #10,-0.23006,0.48061,-0.84622,212.13,0.22993,0.87177,0.43261,-89.291,0.94562,-0.095042,-0.31107,58.162 > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.23006,0.48061,-0.84622,206.51,0.22993,0.87177,0.43261,-81.849,0.94562,-0.095042,-0.31107,43.385 > view matrix models > #10,-0.23006,0.48061,-0.84622,209.88,0.22993,0.87177,0.43261,-83.853,0.94562,-0.095042,-0.31107,44.292 > select subtract #10 Nothing selected > hide #!10 models > hide #!11 models > show #!10 models > hide #!10 models > show #!9 models > show #!10 models > select add #9 2 models selected > view matrix models > #9,0.18919,0.68161,-0.70683,127.56,-0.072128,0.72753,0.68227,-34.663,0.97929,-0.078095,0.1868,-5.196 > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.094504,0.99539,-0.016524,13.65,-0.46578,0.02954,-0.88441,305.71,-0.87984,0.091276,0.46642,193.56 > ui mousemode right ""translate selected models"" > view matrix models > #9,0.094504,0.99539,-0.016524,15.801,-0.46578,0.02954,-0.88441,306.87,-0.87984,0.091276,0.46642,176.78 > view matrix models > #9,0.094504,0.99539,-0.016524,12.042,-0.46578,0.02954,-0.88441,307.73,-0.87984,0.091276,0.46642,167.03 > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.21351,-0.97318,0.085687,220.62,-0.11603,0.061829,0.99132,14.069,-0.97003,-0.2216,-0.099713,290.21 > ui mousemode right ""translate selected models"" > view matrix models > #9,0.21351,-0.97318,0.085687,223.99,-0.11603,0.061829,0.99132,9.6501,-0.97003,-0.2216,-0.099713,279.71 > fitmap #9 inMap #10 Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 29766 points correlation = 0.8261, correlation about mean = 0.3518, overlap = 1268 steps = 228, shift = 10.5, angle = 43.8 degrees Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) relative to cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates: Matrix rotation and translation -0.79231406 -0.50183310 0.34698987 259.09489231 0.60835065 -0.60661249 0.51179172 70.83831660 -0.04634564 0.61659129 0.78591810 -47.09681091 Axis 0.08862868 0.33264264 0.93887903 Axis point 119.55771099 88.88471782 0.00000000 Rotation angle (degrees) 143.75577737 Shift along axis 2.30887434 > select subtract #9 Nothing selected > hide #!9 models > hide #!10 models > show #!9 models > show #!10 models > hide #!10 models > show #!8 models > hide #!9 models > show #!9 models > select add #8 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.57009,0.77789,0.26434,-76.801,0.087184,0.26265,-0.96094,232.01,-0.81694,0.57087,0.081917,150.81 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.57009,0.77789,0.26434,-65.422,0.087184,0.26265,-0.96094,221.32,-0.81694,0.57087,0.081917,140.75 > view matrix models > #8,0.57009,0.77789,0.26434,-76.259,0.087184,0.26265,-0.96094,220.33,-0.81694,0.57087,0.081917,139.28 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.35163,-0.43011,0.83148,20.753,0.096433,0.90012,0.42483,-70.009,-0.93116,-0.069204,0.35799,194.15 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.35163,-0.43011,0.83148,32.249,0.096433,0.90012,0.42483,-69.075,-0.93116,-0.069204,0.35799,199.19 > fitmap #8 inMap #9 Fit map cryosparc_P4_J242_class_00_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc using 14754 points correlation = 0.886, correlation about mean = 0.3322, overlap = 930.7 steps = 164, shift = 11.7, angle = 31.5 degrees Position of cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) relative to cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.99392076 -0.10814474 0.02064566 12.78899705 -0.02517844 -0.40582068 -0.91360584 308.93876287 0.10718010 0.90753198 -0.40607651 52.31471926 Axis 0.99784036 -0.04741407 0.04545901 Axis point 0.00000000 137.80284162 126.13315110 Rotation angle (degrees) 114.14129203 Shift along axis 0.49150880 > select subtract #8 Nothing selected > hide #!9 models > show #!9 models > hide #!8 models > show #!8 models > hide #!9 models > view P1 > show #!9 models > hide #!8 models > hide #!9 models > show #!10 models > hide #!10 models > show #!11 models > hide #!11 models > show #!12 models > hide #!12 models > show #!8 models > show #!12 models > view P1 > select add #8 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.17056,0.37082,0.91291,-61.936,0.033776,0.92374,-0.38153,50.195,-0.98477,0.095906,0.14502,217.51 > select subtract #8 Nothing selected > hide #!12 models > show #!9 models > select add #9 2 models selected > view matrix models > #9,0.22431,-0.86548,-0.44791,277.63,0.10958,-0.43431,0.89407,50.356,-0.96834,-0.24963,-0.0025846,282.76 > fitmap #9 inMap #8 Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_00_00122_volume_sharp.mrc using 29766 points correlation = 0.8496, correlation about mean = 0.3079, overlap = 1328 steps = 196, shift = 4.92, angle = 23.1 degrees Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) relative to cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) coordinates: Matrix rotation and translation 0.99577299 -0.02696715 0.08780046 -8.42294333 -0.09023986 -0.46536786 0.88050527 89.20116331 0.01711480 -0.88470646 -0.46583426 307.74421532 Axis -0.99855897 0.03998603 -0.03579261 Axis point 0.00000000 137.24012810 127.13677639 Rotation angle (degrees) 117.88604570 Shift along axis 0.96263749 > select subtract #9 Nothing selected > select add #9 2 models selected > select subtract #9 Nothing selected > hide #!8 models > hide #!9 models > show #!9 models > show #!10 models > show #!8 models > hide #!9 models > hide #!8 models > show #!9 models > select add #10 2 models selected > view matrix models > #10,-0.15057,0.45945,-0.87535,204.11,-0.21614,0.84872,0.48265,-19.059,0.96468,0.26187,-0.028487,-39.785 > fitmap #10 inMap #8 Fit map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_00_00122_volume_sharp.mrc using 20970 points correlation = 0.8656, correlation about mean = 0.3963, overlap = 1232 steps = 148, shift = 6.34, angle = 30.8 degrees Position of cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) relative to cryosparc_P4_J242_class_00_00122_volume_sharp.mrc (#8) coordinates: Matrix rotation and translation -0.99459983 0.06769619 -0.07866640 263.08124995 0.09074118 0.93510189 -0.34256458 42.75279763 0.05037079 -0.34785296 -0.93619501 298.73878944 Axis -0.04031220 -0.98362390 0.17566718 Axis point 125.67832095 0.00000000 157.57753081 Rotation angle (degrees) 176.23911220 Shift along axis -0.17945663 > show #!8 models > hide #!9 models > select subtract #10 Nothing selected > hide #!10 models > show #!10 models > hide #!8 models > show #!8 models > hide #!8 models > show #!11 models > hide #!10 models > show #!10 models > select add #11 2 models selected > view matrix models > #11,0.83789,-0.53148,-0.12435,93.216,-0.53452,-0.84509,0.010318,306.1,-0.11057,0.05782,-0.99219,291.46 > view matrix models > #11,0.87567,0.38049,0.29737,-84.014,0.47018,-0.53126,-0.70477,229.85,-0.11018,0.75696,-0.64411,156.03 > view matrix models > #11,0.99273,0.070823,-0.097356,-6.1982,0.016369,-0.88055,-0.47367,302.86,-0.11927,0.46863,-0.87531,225.51 > fitmap #11 inMap #10 Fit map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 45754 points correlation = 0.7386, correlation about mean = -0.02581, overlap = 1355 steps = 168, shift = 17.3, angle = 31.8 degrees Position of cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) relative to cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates: Matrix rotation and translation -0.38917965 0.05095816 -0.91975131 323.90582539 -0.15837916 -0.98730156 0.01231516 285.52055130 -0.90744434 0.15046225 0.39230839 175.68159882 Axis 0.55013716 -0.04900950 -0.83363492 Axis point 230.74773970 125.72052254 0.00000000 Rotation angle (degrees) 172.78707980 Shift along axis 17.74509610 > select subtract #11 Nothing selected > hide #!11 models > hide #!10 models > show #!11 models > hide #!11 models > show #!10 models > hide #!10 models > show #!9 models > hide #!9 models > view P1 > show #!12 models > ui mousemode right translate > save P4_J242_class_4_sharp.png supersample 3 transparentBackground true > hide #!12 models > show #!11 models > save P4_J242_class_3_sharp.png supersample 3 transparentBackground true > hide #!11 models > show #!10 models > save P4_J242_class_2_sharp.png supersample 3 transparentBackground true > hide #!10 models > show #!9 models > view P1 [Repeated 1 time(s)] > save P4_J242_class_1_sharp.png supersample 3 transparentBackground true > hide #!9 models > show #!8 models > save P4_J242_class_0_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow.cxs"" Unsupported scale factor (0.000000) detected on Display1 [Repeated 2 time(s)] > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J117_class_00_00162_volume_sharp.mrc"" Opened cryosparc_P4_J117_class_00_00162_volume_sharp.mrc as #13, grid size 128,128,128, pixel 2.08, shown at level 0.163, step 1, values float32 > hide #!8 models > select add #13 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #13,1,0,0,6.2015,0,1,0,0.69431,0,0,1,-17.516 > ui mousemode right ""rotate selected models"" > view matrix models > #13,-0.13264,-0.68512,-0.71625,337.99,0.0019176,-0.72281,0.69104,120.39,-0.99116,0.090284,0.097186,224.71 > view matrix models > #13,0.0040424,0.12352,-0.99233,257.27,0.14964,-0.98124,-0.12153,245.92,-0.98873,-0.148,-0.02245,270.75 > select subtract #13 Nothing selected > show #!12 models > hide #!12 models > show #!11 models > hide #!11 models > show #!10 models > fitmap #13 inMap #10 Fit map cryosparc_P4_J117_class_00_00162_volume_sharp.mrc in map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 20961 points correlation = 0.8109, correlation about mean = 0.2077, overlap = 1054 steps = 92, shift = 12.7, angle = 18.1 degrees Position of cryosparc_P4_J117_class_00_00162_volume_sharp.mrc (#13) relative to cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates: Matrix rotation and translation -0.98193657 -0.07856914 0.17212633 243.32837219 0.00195692 -0.91387700 -0.40598645 309.66348462 0.18920029 -0.39831610 0.89752300 41.87114917 Axis 0.09277951 -0.20652448 0.97403265 Axis point 116.38449758 161.85402651 0.00000000 Rotation angle (degrees) 177.63092236 Shift along axis -0.59333628 > hide #!10 models > hide #!13 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J117_class_01_00162_volume_sharp.mrc"" Opened cryosparc_P4_J117_class_01_00162_volume_sharp.mrc as #14, grid size 128,128,128, pixel 2.08, shown at level 0.187, step 1, values float32 > select add #14 2 models selected > view matrix models > #14,-0.39254,-0.77748,0.49135,234.79,-0.04345,-0.51796,-0.8543,320.26,0.91871,-0.3567,0.16954,27.288 > view matrix models > #14,-0.061348,0.89979,0.432,-25.376,-0.288,-0.43036,0.85548,115.2,0.95566,-0.071931,0.28554,-30.976 > view matrix models > #14,-0.046716,0.65995,-0.74985,161.94,-0.070464,0.74662,0.6615,-44.914,0.99642,0.08374,0.011624,-20.712 > select subtract #14 Nothing selected > show #!13 models > fitmap #14 inMap #13 Fit map cryosparc_P4_J117_class_01_00162_volume_sharp.mrc in map cryosparc_P4_J117_class_00_00162_volume_sharp.mrc using 20968 points correlation = 0.846, correlation about mean = 0.3465, overlap = 1110 steps = 132, shift = 18.5, angle = 19.5 degrees Position of cryosparc_P4_J117_class_01_00162_volume_sharp.mrc (#14) relative to cryosparc_P4_J117_class_00_00162_volume_sharp.mrc (#13) coordinates: Matrix rotation and translation -0.99955515 0.02982234 0.00035424 260.68209471 -0.00628473 -0.19900464 -0.97997839 284.54003350 -0.02915475 -0.97954468 0.19910354 244.04930876 Axis 0.00930049 0.63278447 -0.77427212 Axis point 133.98017190 240.03303746 0.00000000 Rotation angle (degrees) 178.66392593 Shift along axis -6.48359029 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J117_class_02_00162_volume_sharp.mrc"" Opened cryosparc_P4_J117_class_02_00162_volume_sharp.mrc as #15, grid size 128,128,128, pixel 2.08, shown at level 0.251, step 1, values float32 > hide #!13 models > select add #14 2 models selected > show #!12 models > select subtract #14 Nothing selected > hide #!14 models > select add #15 2 models selected > view matrix models > #15,-0.98221,0.18526,0.030552,219.51,0.18651,0.98144,0.044675,-26.394,-0.021708,0.049578,-0.99853,243.73 > ui mousemode right ""translate selected models"" > view matrix models > #15,-0.98221,0.18526,0.030552,234.62,0.18651,0.98144,0.044675,-36.86,-0.021708,0.049578,-0.99853,271.78 > fitmap #15 inMap #12 Fit map cryosparc_P4_J117_class_02_00162_volume_sharp.mrc in map cryosparc_P4_J242_class_04_00122_volume_sharp.mrc using 20967 points correlation = 0.781, correlation about mean = 0.07908, overlap = 1573 steps = 76, shift = 10.9, angle = 6.65 degrees Position of cryosparc_P4_J117_class_02_00162_volume_sharp.mrc (#15) relative to cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.82536305 0.56130744 0.06090799 -57.36751075 -0.56057744 0.82755504 -0.03009290 101.38226037 -0.06729608 -0.00930608 0.99768964 1.14989876 Axis 0.01840555 0.11351744 -0.99336550 Axis point 134.55599767 144.37243816 0.00000000 Rotation angle (degrees) 34.38068857 Shift along axis 9.31050435 > volume flip #15 Opened cryosparc_P4_J117_class_02_00162_volume_sharp.mrc z flip as #16, grid size 128,128,128, pixel 2.08, shown at step 1, values float32 > close #15 > select add #16 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #16,-0.81511,-0.57721,0.04929,312.41,0.52972,-0.77708,-0.33992,218.14,0.2345,-0.25096,0.93916,8.6526 > fitmap #15 inMap #12 No atoms or maps for #15 > fitmap #16 inMap #12 Fit map cryosparc_P4_J117_class_02_00162_volume_sharp.mrc z flip in map cryosparc_P4_J242_class_04_00122_volume_sharp.mrc using 20967 points correlation = 0.9777, correlation about mean = 0.7437, overlap = 2747 steps = 108, shift = 14.1, angle = 17.5 degrees Position of cryosparc_P4_J117_class_02_00162_volume_sharp.mrc z flip (#16) relative to cryosparc_P4_J242_class_04_00122_volume_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.94024990 -0.32652551 -0.09649458 65.60674301 -0.33221344 -0.94188358 -0.04989541 307.74881291 -0.07459454 0.07897095 -0.99408211 253.25354142 Axis 0.98493295 -0.16738329 -0.04347315 Axis point 0.00000000 155.23786381 133.19610246 Rotation angle (degrees) 176.24909728 Shift along axis 2.09650544 > select subtract #16 Nothing selected > rename #16 CS_P4_J117_class_02_sharp_flip.mrc id #15 > save CS_P4_J117_class_02_sharp_flip.mrc #15 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J117_class_03_00162_volume_sharp.mrc"" Opened cryosparc_P4_J117_class_03_00162_volume_sharp.mrc as #16, grid size 128,128,128, pixel 2.08, shown at level 0.179, step 1, values float32 > hide #!12 models > hide #!15 models > select add #16 2 models selected > show #!14 models > view matrix models > #16,0.00021536,0.34795,0.93751,-37.63,0.50671,0.80821,-0.30007,0.053261,-0.86212,0.47511,-0.17613,183.13 > hide #!14 models > view matrix models > #16,0.63015,0.10301,-0.76961,125.95,-0.74582,0.35606,-0.56301,261.02,0.21603,0.92877,0.3012,-81.743 > view matrix models > #16,0.63277,-0.43368,-0.64151,190.37,0.75188,0.14602,0.64293,-47.242,-0.18515,-0.88916,0.41847,227.83 > show #!13 models > hide #!13 models > show #!12 models > hide #!12 models > show #!11 models > ui mousemode right ""translate selected models"" > view matrix models > #16,0.63277,-0.43368,-0.64151,206.09,0.75188,0.14602,0.64293,-70.694,-0.18515,-0.88916,0.41847,249.05 > view matrix models > #16,0.63277,-0.43368,-0.64151,204.5,0.75188,0.14602,0.64293,-75.196,-0.18515,-0.88916,0.41847,240.94 > ui mousemode right ""rotate selected models"" > view matrix models > #16,-0.30976,-0.38252,-0.87047,346.06,0.94397,-0.2334,-0.23335,63.654,-0.1139,-0.89398,0.43339,230.67 > fitmap #16 inMap #11 Fit map cryosparc_P4_J117_class_03_00162_volume_sharp.mrc in map cryosparc_P4_J242_class_03_00122_volume_sharp.mrc using 20958 points correlation = 0.9023, correlation about mean = 0.3197, overlap = 1117 steps = 184, shift = 6.54, angle = 53.8 degrees Position of cryosparc_P4_J117_class_03_00162_volume_sharp.mrc (#16) relative to cryosparc_P4_J242_class_03_00122_volume_sharp.mrc (#11) coordinates: Matrix rotation and translation 0.41743274 -0.19488532 -0.88756388 222.32976103 -0.90862481 -0.10271919 -0.40478358 322.57606660 -0.01228347 0.97543246 -0.21995599 21.59894000 Axis 0.77392148 -0.49079151 -0.40021149 Axis point 0.00000000 222.40854643 197.20887777 Rotation angle (degrees) 116.91198346 Shift along axis 5.10403978 > select subtract #16 Nothing selected > hide #!11 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J117_class_04_00162_volume_sharp.mrc"" Opened cryosparc_P4_J117_class_04_00162_volume_sharp.mrc as #17, grid size 128,128,128, pixel 2.08, shown at level 0.206, step 1, values float32 > hide #!16 models > select add #17 2 models selected > show #!13 models > hide #!13 models > show #!11 models > hide #!11 models > show #!10 models > hide #!17 models > show #!17 models > view matrix models > #17,-0.0034658,-0.079884,-0.9968,294.42,-0.15421,0.98492,-0.078396,35.543,0.98803,0.15344,-0.015732,-30.795 > fitmap #17 inMap #10 Fit map cryosparc_P4_J117_class_04_00162_volume_sharp.mrc in map cryosparc_P4_J242_class_02_00122_volume_sharp.mrc using 20958 points correlation = 0.8416, correlation about mean = 0.3036, overlap = 1170 steps = 148, shift = 13.9, angle = 32.2 degrees Position of cryosparc_P4_J117_class_04_00162_volume_sharp.mrc (#17) relative to cryosparc_P4_J242_class_02_00122_volume_sharp.mrc (#10) coordinates: Matrix rotation and translation 0.73519379 0.67627298 0.04631360 -60.93633283 -0.67522557 0.73664284 -0.03778583 134.15115598 -0.05967011 -0.00349222 0.99821205 3.94076312 Axis 0.02528875 0.07815439 -0.99662047 Axis point 141.29888305 145.62167557 0.00000000 Rotation angle (degrees) 42.69072745 Shift along axis 5.01605257 > select subtract #17 Nothing selected > hide #!10 models > show #!10 models > hide #!17 models > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow.cxs"" > show #!13 models > hide #!10 models > color #13 #FCEDFF > hide #!13 models > show #!14 models > color #14 #FCEDFF > show #!15 models > hide #!14 models > hide #!15 models > show #!16 models > color #16 #FCEDFF > hide #!16 models > show #!17 models > color #17 #FCEDFF > show #!15 models > hide #!17 models > color #15 #99BFE5 > volume #15 level 0.3349 > ui mousemode right translate > view P1 [Repeated 1 time(s)] > save P4_J117_class_2_sharp.png supersample 3 transparentBackground true > hide #!15 models > show #!13 models > save P4_J117_class_0_sharp.png supersample 3 transparentBackground true > hide #!13 models > show #!14 models > save P4_J117_class_1_sharp.png supersample 3 transparentBackground true > hide #!14 models > show #!16 models > save P4_J117_class_3_sharp.png supersample 3 transparentBackground true > hide #!16 models > show #!17 models > save P4_J117_class_4_sharp.png supersample 3 transparentBackground true [Repeated 1 time(s)] > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J120_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J120_002_volume_map_sharp.mrc as #18, grid size 80,80,80, pixel 3.32, shown at level 1.08, step 1, values float32 > hide #!17 models > show #!15 models > select add #18 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #18,0.9199,0.35329,0.17023,-57.439,0.37414,-0.92071,-0.11099,219.04,0.11752,0.16579,-0.97913,208.75 > ui mousemode right ""translate selected models"" > view matrix models > #18,0.9199,0.35329,0.17023,-56.147,0.37414,-0.92071,-0.11099,218.08,0.11752,0.16579,-0.97913,234.23 > ui mousemode right ""rotate selected models"" > view matrix models > #18,0.47537,0.87487,0.092902,-59.652,0.86989,-0.48319,0.099115,73.008,0.1316,0.033698,-0.99073,251.23 > volume flip #18 Opened cryosparc_P4_J120_002_volume_map_sharp.mrc z flip as #19, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > select subtract #18 Nothing selected > close #18 > select add #19 2 models selected > view matrix models > #19,0.011836,0.9987,-0.049536,1.5471,-0.96239,0.024824,0.27053,210.58,0.27141,0.044471,0.96144,-38.44 > ui mousemode right ""translate selected models"" > view matrix models > #19,0.011836,0.9987,-0.049536,5.1894,-0.96239,0.024824,0.27053,209.75,0.27141,0.044471,0.96144,-23.291 > fitmap #19 inMap #15 Fit map cryosparc_P4_J120_002_volume_map_sharp.mrc z flip in map CS_P4_J117_class_02_sharp_flip.mrc using 5118 points correlation = 0.9182, correlation about mean = 0.533, overlap = 3573 steps = 76, shift = 9.96, angle = 10.7 degrees Position of cryosparc_P4_J120_002_volume_map_sharp.mrc z flip (#19) relative to CS_P4_J117_class_02_sharp_flip.mrc (#15) coordinates: Matrix rotation and translation -0.48058823 -0.86458262 0.14673736 288.72558748 0.85464108 -0.49926017 -0.14257599 104.76974006 0.19652884 0.05688743 0.97884638 -28.97188121 Axis 0.11519876 -0.02875674 0.99292613 Axis point 115.59153027 135.80137987 0.00000000 Rotation angle (degrees) 120.03315219 Shift along axis 1.48105620 > ui mousemode right ""rotate selected models"" > view matrix models > #19,0.89305,-0.32489,-0.3113,106.99,0.34183,0.93976,-0.00013805,-25.175,0.29259,-0.10629,0.95031,-3.3753 > ui mousemode right ""translate selected models"" > view matrix models > #19,0.89305,-0.32489,-0.3113,96.178,0.34183,0.93976,-0.00013805,-42.263,0.29259,-0.10629,0.95031,-5.1551 > fitmap #19 inMap #15 Fit map cryosparc_P4_J120_002_volume_map_sharp.mrc z flip in map CS_P4_J117_class_02_sharp_flip.mrc using 5118 points correlation = 0.9187, correlation about mean = 0.5356, overlap = 3578 steps = 76, shift = 8.31, angle = 8.52 degrees Position of cryosparc_P4_J120_002_volume_map_sharp.mrc z flip (#19) relative to CS_P4_J117_class_02_sharp_flip.mrc (#15) coordinates: Matrix rotation and translation -0.47913034 0.85546358 0.19651003 54.96243137 -0.86530880 -0.49790427 0.05772364 303.37608678 0.14722365 -0.14238471 0.97880120 3.73022055 Axis -0.11546470 0.02843878 -0.99290440 Axis point 115.58296139 135.79077530 0.00000000 Rotation angle (degrees) 119.94157891 Shift along axis -1.42232844 > hide #!19 models > hide #!15 models > show #!15 models > hide #!15 models > show #!19 models > select subtract #19 Nothing selected > show #!15 models > hide #!15 models > rename #19 CS_P4_J120_sharp_flip id #18 > save CS_P4_J120_sharp_flip.mrc #18 > volume #18 level 1.185 > volume #18 level 1.639 > volume #18 step 2 > volume #18 step 1 > show #!15 models > volume #18 level 1.559 > hide #!15 models > volume #18 level 1.292 > view P1 > color #18 #99BFE5 > show #!17 models > hide #!17 models > hide #!18 models > show #!18 models > save P4_J120_NU_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J169_class_00_00182_volume_sharp.mrc"" Opened cryosparc_P4_J169_class_00_00182_volume_sharp.mrc as #19, grid size 128,128,128, pixel 2.08, shown at level 0.175, step 1, values float32 > select add #19 2 models selected > hide #!18 models > show #!18 models > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models #19,1,0,0,-7.1681,0,1,0,-1.6755,0,0,1,29.407 > fitmap #19 inMap #18 Fit map cryosparc_P4_J169_class_00_00182_volume_sharp.mrc in map CS_P4_J120_sharp_flip.mrc using 20970 points correlation = 0.3797, correlation about mean = 0.05313, overlap = 2374 steps = 192, shift = 6.4, angle = 17.5 degrees Position of cryosparc_P4_J169_class_00_00182_volume_sharp.mrc (#19) relative to CS_P4_J120_sharp_flip.mrc (#18) coordinates: Matrix rotation and translation 0.64594502 0.66965380 0.36649532 -93.21942227 -0.65111130 0.73392063 -0.19342850 149.32350272 -0.39850860 -0.11368507 0.91009153 102.27587247 Axis 0.05217441 0.50052557 -0.86414813 Axis point 153.99219258 219.18137479 0.00000000 Rotation angle (degrees) 49.83592965 Shift along axis -18.50494005 > select subtract #19 Nothing selected > hide #!18 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J169_class_01_00182_volume_sharp.mrc"" Opened cryosparc_P4_J169_class_01_00182_volume_sharp.mrc as #20, grid size 128,128,128, pixel 2.08, shown at level 0.189, step 1, values float32 > hide #!19 models > show #!17 models > select add #20 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #20,0.023382,0.1088,0.99379,-27.517,0.050205,0.99268,-0.10986,9.6432,-0.99847,0.052462,0.017749,251.64 > hide #!17 models > show #!16 models > hide #!16 models > show #!15 models > hide #!15 models > show #!14 models > ui mousemode right ""translate selected models"" > view matrix models > #20,0.023382,0.1088,0.99379,-22.964,0.050205,0.99268,-0.10986,7.1023,-0.99847,0.052462,0.017749,242.74 > ui mousemode right ""rotate selected models"" > view matrix models > #20,-0.029978,-0.71994,-0.69339,335.92,-0.21064,-0.67357,0.70847,177,-0.9771,0.16729,-0.13145,243.19 > ui mousemode right ""translate selected models"" > view matrix models > #20,-0.029978,-0.71994,-0.69339,328.25,-0.21064,-0.67357,0.70847,170.9,-0.9771,0.16729,-0.13145,240.41 > fitmap #20 inMap #14 Fit map cryosparc_P4_J169_class_01_00182_volume_sharp.mrc in map cryosparc_P4_J117_class_01_00162_volume_sharp.mrc using 20954 points correlation = 0.8829, correlation about mean = 0.4124, overlap = 1200 steps = 104, shift = 14, angle = 14 degrees Position of cryosparc_P4_J169_class_01_00182_volume_sharp.mrc (#20) relative to cryosparc_P4_J117_class_01_00162_volume_sharp.mrc (#14) coordinates: Matrix rotation and translation -0.94773816 0.28655181 -0.14028702 243.79600144 -0.24891252 -0.93914826 -0.23673424 326.23627964 -0.19958693 -0.18944287 0.96139298 60.20896934 Axis 0.08744550 0.10965027 -0.99011621 Axis point 147.27291182 149.47535150 0.00000000 Rotation angle (degrees) 164.31164420 Shift along axis -2.52311906 > select subtract #20 Nothing selected > hide #!14 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J169_class_02_00182_volume_sharp.mrc"" Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #21, grid size 128,128,128, pixel 2.08, shown at level 0.216, step 1, values float32 > hide #!20 models > select add #21 2 models selected > view matrix models #21,1,0,0,-13.073,0,1,0,8.3491,0,0,1,8.6967 > ui mousemode right ""rotate selected models"" > view matrix models > #21,-0.06365,0.67952,0.73089,-53.58,-0.2928,0.68743,-0.66461,177.89,-0.95405,-0.25631,0.15521,285.48 > view matrix models > #21,0.10048,-0.44353,0.89061,41.096,0.13793,-0.88029,-0.45395,284.46,0.98533,0.16846,-0.027275,-4.3073 > fitmap #21 inMap #20 Fit map cryosparc_P4_J169_class_02_00182_volume_sharp.mrc in map cryosparc_P4_J169_class_01_00182_volume_sharp.mrc using 20962 points correlation = 0.7829, correlation about mean = 0.1539, overlap = 900.6 steps = 188, shift = 21.5, angle = 32 degrees Position of cryosparc_P4_J169_class_02_00182_volume_sharp.mrc (#21) relative to cryosparc_P4_J169_class_01_00182_volume_sharp.mrc (#20) coordinates: Matrix rotation and translation -0.75680258 0.56772680 0.32393846 109.96194933 0.37589927 0.78345603 -0.49487007 56.85693302 -0.53474254 -0.25275071 -0.80632963 338.09031391 Axis 0.26532092 0.94096581 -0.21020979 Axis point 90.65236627 0.00000000 161.68382083 Rotation angle (degrees) 152.85290905 Shift along axis 11.60574300 > show #!20 models > select subtract #21 Nothing selected > select add #21 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #21,0.31625,-0.43913,0.84092,24.723,-0.35094,-0.87769,-0.32634,336.73,0.88138,-0.19191,-0.43168,94.219 > ui mousemode right ""rotate selected models"" > view matrix models > #21,0.23561,0.79493,-0.55908,75.399,0.21977,0.51679,0.82742,-71.321,0.94667,-0.31782,-0.052938,48.925 > ui mousemode right ""translate selected models"" > view matrix models > #21,0.23561,0.79493,-0.55908,69.861,0.21977,0.51679,0.82742,-70.077,0.94667,-0.31782,-0.052938,40.098 > fitmap #21 inMap #20 Fit map cryosparc_P4_J169_class_02_00182_volume_sharp.mrc in map cryosparc_P4_J169_class_01_00182_volume_sharp.mrc using 20962 points correlation = 0.8883, correlation about mean = 0.4082, overlap = 1398 steps = 80, shift = 8.95, angle = 4.79 degrees Position of cryosparc_P4_J169_class_02_00182_volume_sharp.mrc (#21) relative to cryosparc_P4_J169_class_01_00182_volume_sharp.mrc (#20) coordinates: Matrix rotation and translation -0.99875153 -0.02706229 -0.04198798 281.31180443 0.03395891 -0.98426911 -0.17338138 286.61926959 -0.03663538 -0.17459079 0.98395929 28.58358251 Axis -0.01973976 -0.08736459 0.99598081 Axis point 138.73615561 146.72655614 0.00000000 Rotation angle (degrees) 178.24454217 Shift along axis -2.12470384 > select subtract #21 Nothing selected > hide #!20 models > hide #!21 models > show #!21 models > show #!20 models > hide #!21 models > show #!21 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J169_class_03_00182_volume_sharp.mrc"" Opened cryosparc_P4_J169_class_03_00182_volume_sharp.mrc as #22, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 > hide #!20 models > hide #!21 models > select add #22 2 models selected > show #!18 models > ui mousemode right ""rotate selected models"" > view matrix models > #22,0.80286,-0.54835,0.23395,74.113,-0.54307,-0.83458,-0.092472,336.96,0.24595,-0.052807,-0.96784,209.56 > view matrix models > #22,0.23802,0.97115,0.01476,-30.605,0.97056,-0.2384,0.03436,32.801,0.036887,0.0061467,-0.9993,233.87 > ui mousemode right ""translate selected models"" > view matrix models > #22,0.23802,0.97115,0.01476,-35.135,0.97056,-0.2384,0.03436,31.843,0.036887,0.0061467,-0.9993,265.72 > view matrix models > #22,0.23802,0.97115,0.01476,-30.091,0.97056,-0.2384,0.03436,32.303,0.036887,0.0061467,-0.9993,265.71 > select subtract #22 Nothing selected > hide #!18 models > volume flip #22 Opened cryosparc_P4_J169_class_03_00182_volume_sharp.mrc z flip as #23, grid size 128,128,128, pixel 2.08, shown at step 1, values float32 > close #22 > show #!21 models > hide #!21 models > show #!18 models > select add #23 2 models selected > view matrix models > #23,0.23802,0.97115,0.01476,-34.192,0.97056,-0.2384,0.03436,27.412,0.036887,0.0061467,-0.9993,278.73 > ui mousemode right ""rotate selected models"" > view matrix models > #23,-0.23315,-0.92003,-0.31494,337.04,0.93397,-0.30205,0.19095,18.61,-0.27081,-0.24962,0.92971,78.293 > ui mousemode right ""translate selected models"" > view matrix models > #23,-0.23315,-0.92003,-0.31494,335.86,0.93397,-0.30205,0.19095,18.866,-0.27081,-0.24962,0.92971,88.616 > fitmap #23 inMap #18 Fit map cryosparc_P4_J169_class_03_00182_volume_sharp.mrc z flip in map CS_P4_J120_sharp_flip.mrc using 20952 points correlation = 0.9077, correlation about mean = 0.6695, overlap = 1.202e+04 steps = 60, shift = 4.34, angle = 10.2 degrees Position of cryosparc_P4_J169_class_03_00182_volume_sharp.mrc z flip (#23) relative to CS_P4_J120_sharp_flip.mrc (#18) coordinates: Matrix rotation and translation 0.17479617 -0.97573598 0.13185442 219.49728105 0.98179238 0.18284123 0.05150543 -32.00811477 -0.07436413 0.12045072 0.98993010 -9.54926019 Axis 0.03500529 0.10470244 0.99388733 Axis point 128.78581299 116.22335978 0.00000000 Rotation angle (degrees) 79.99211268 Shift along axis -5.15865059 > select subtract #23 Nothing selected > hide #!18 models > rename #23 CS_P4_J169_class_03_sharp_flip id #22 > save CS_P4_J169_class_03_sharp_flip.mrc #22 > show #!21 models > hide #!21 models > show #!18 models > hide #!18 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J169_class_04_00182_volume_sharp.mrc"" Opened cryosparc_P4_J169_class_04_00182_volume_sharp.mrc as #23, grid size 128,128,128, pixel 2.08, shown at level 0.171, step 1, values float32 > hide #!22 models > show #!21 models > select add #23 2 models selected > view matrix models #23,1,0,0,62.54,0,1,0,-0.93224,0,0,1,-9.0713 > ui mousemode right ""rotate selected models"" > view matrix models > #23,0.11131,-0.99321,-0.033862,304.62,-0.95598,-0.11633,0.2694,223.09,-0.27151,0.0023841,-0.96243,297.1 > view matrix models > #23,0.14785,0.8725,0.4657,-3.2346,-0.24604,0.48852,-0.83714,210.48,-0.95792,0.0091875,0.2869,210.23 > ui mousemode right ""translate selected models"" > view matrix models > #23,0.14785,0.8725,0.4657,-72.613,-0.24604,0.48852,-0.83714,211.81,-0.95792,0.0091875,0.2869,205.44 > ui mousemode right ""rotate selected models"" > view matrix models > #23,-0.12372,0.72067,0.68215,-49.094,0.065146,0.69184,-0.7191,130.45,-0.99018,-0.044529,-0.13254,274.4 > ui mousemode right ""translate selected models"" > view matrix models > #23,-0.12372,0.72067,0.68215,-52.059,0.065146,0.69184,-0.7191,130.58,-0.99018,-0.044529,-0.13254,270.2 > fitmap #23 inMap #21 Fit map cryosparc_P4_J169_class_04_00182_volume_sharp.mrc in map cryosparc_P4_J169_class_02_00182_volume_sharp.mrc using 20956 points correlation = 0.8996, correlation about mean = 0.4033, overlap = 1373 steps = 168, shift = 14.7, angle = 39.5 degrees Position of cryosparc_P4_J169_class_04_00182_volume_sharp.mrc (#23) relative to cryosparc_P4_J169_class_02_00182_volume_sharp.mrc (#21) coordinates: Matrix rotation and translation -0.99961182 0.01552465 -0.02313457 267.26750037 0.02397017 0.90245504 -0.43011668 70.06567251 0.01420050 -0.43050425 -0.90247684 305.57661651 Axis -0.01012464 -0.97530665 0.22062281 Axis point 131.76679627 0.00000000 162.02424501 Rotation angle (degrees) 178.90328205 Shift along axis -3.62433410 > select subtract #23 Nothing selected > hide #!23 models > hide #!21 models > show #!23 models > volume #23 level 0.1996 > hide #!23 models > show #!22 models > volume #22 level 0.2715 > hide #!22 models > show #!21 models > volume #21 level 0.2481 > hide #!21 models > show #!20 models > volume #20 level 0.198 > hide #!20 models > show #!19 models > volume #19 level 0.1357 > volume #19 level 0.1565 > color #9 #FCEDFF > show #!9 models > hide #!9 models > color #19 #FCEDFF > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow.cxs"" > hide #!19 models > show #!20 models > color #20 #FCEDFF > hide #!20 models > show #!21 models > show #!20 models > hide #!20 models > color #21 #FCEDFF > hide #!21 models > show #!22 models > show #!23 models > hide #!22 models > color #23 #FCEDFF > color #22 #99BFE5 > show #!22 models > hide #!23 models > hide #!22 models > show #!22 models > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow.cxs"" > view P1 > save P4_J169_class_3_sharp.png supersample 3 transparentBackground true > hide #!22 models > show #!19 models > save P4_J169_class_0_sharp.png supersample 3 transparentBackground true > hide #!19 models > show #!20 models > save P4_J169_class_1_sharp.png supersample 3 transparentBackground true > hide #!20 models > show #!21 models > save P4_J169_class_2_sharp.png supersample 3 transparentBackground true > hide #!21 models > show #!22 models > show #!23 models > hide #!22 models > save P4_J169_class_4_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J176_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J176_002_volume_map_sharp.mrc as #24, grid size 80,80,80, pixel 3.32, shown at level 1.05, step 1, values float32 > show #!22 models > hide #!23 models > select add #24 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #24,0.60544,-0.7944,-0.048687,168.77,-0.79404,-0.60707,0.031193,325.29,-0.054337,0.019774,-0.99833,244.32 > view matrix models > #24,0.59955,-0.80023,-0.012763,166.07,-0.79939,-0.59954,0.03913,324.05,-0.038965,-0.013258,-0.99915,246.8 > view matrix models > #24,0.55506,-0.74882,-0.36218,207.08,-0.8209,-0.56341,-0.093219,337.96,-0.13425,0.34906,-0.92744,201.93 > view matrix models > #24,0.18767,0.98161,-0.034938,-17.516,0.95411,-0.19063,-0.23093,58.314,-0.23335,0.010004,-0.97234,267.28 > volume flip #24 Opened cryosparc_P4_J176_002_volume_map_sharp.mrc z flip as #25, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #24 > select add #25 2 models selected > view matrix models > #25,-0.63444,0.77032,-0.064025,129.07,-0.77136,-0.63629,-0.011971,326.31,-0.04996,0.041792,0.99788,-43.633 > ui mousemode right ""translate selected models"" > view matrix models > #25,-0.63444,0.77032,-0.064025,133.77,-0.77136,-0.63629,-0.011971,326.45,-0.04996,0.041792,0.99788,5.2846 > fitmap #25 inMap #22 Fit map cryosparc_P4_J176_002_volume_map_sharp.mrc z flip in map CS_P4_J169_class_03_sharp_flip.mrc using 5115 points correlation = 0.927, correlation about mean = 0.5943, overlap = 3935 steps = 92, shift = 11.4, angle = 9.34 degrees Position of cryosparc_P4_J176_002_volume_map_sharp.mrc z flip (#25) relative to CS_P4_J169_class_03_sharp_flip.mrc (#22) coordinates: Matrix rotation and translation -0.48979714 -0.86290735 -0.12445753 333.02911722 0.86312907 -0.50006428 0.07031310 74.16708713 -0.12291046 -0.07298376 0.98973047 29.10111268 Axis -0.08273609 -0.00089324 0.99657109 Axis point 146.24021491 133.58927656 0.00000000 Rotation angle (degrees) 120.00433179 Shift along axis 1.38155071 > select subtract #25 Nothing selected > rename #25 CS_P4_J176_NU_sharp_flip id #24 > save CS_P4_J176_NU_sharp_flip.mrc #24 > hide #!22 models > volume #24 level 1.757 > volume #24 level 1.364 > color #24 #99BFE5 > volume #24 level 1.6 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow.cxs"" > view P1 > save CS_P4_J176_NU_sharp.png supersample 3 transparentBackground true > open ""/Users/peiyuyu/Documents/Goethe University/19. Model Building/2. AcrF > Project/1. Apo-form/LG-F_Apo/Map/cryosparc_P10_J41_007_volume_map_sharp.mrc"" Opened cryosparc_P10_J41_007_volume_map_sharp.mrc as #25, grid size 320,320,320, pixel 0.831, shown at level 0.123, step 2, values float32 > hide #!24 models > show #!22 models > hide #!22 models > volume #25 level 0.2164 > save CS_P10_J41_NU_sharp_flip.mrc #25 > close #25 > show #!24 models > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260501_SA-F_B1_workflow1.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J255_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J255_002_volume_map_sharp.mrc as #25, grid size 80,80,80, pixel 3.32, shown at level 0.649, step 1, values float32 > hide #!24 models > volume flip #25 Opened cryosparc_P4_J255_002_volume_map_sharp.mrc z flip as #26, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #25 > rename CS_P4_J255_sharp_flip id #25 Missing or invalid ""models"" argument: invalid models specifier > rename #26 CS_P4_J255_sharp_flip id #25 > save CS_P4_J255_sharp_flip.mrc #25 > show #!21 models > hide #!21 models > show #!24 models > fitmap #25 inMap #24 Fit map CS_P4_J255_sharp_flip.mrc in map CS_P4_J176_NU_sharp_flip.mrc using 5116 points correlation = 0.3392, correlation about mean = 0.06206, overlap = 2168 steps = 64, shift = 8.32, angle = 5.45 degrees Position of CS_P4_J255_sharp_flip.mrc (#25) relative to CS_P4_J176_NU_sharp_flip.mrc (#24) coordinates: Matrix rotation and translation -0.61720035 -0.75989860 -0.20400451 353.05950420 0.73150715 -0.64968488 0.20689815 96.93395715 -0.28976026 -0.02153315 0.95685700 43.12583281 Axis -0.15115555 0.05674554 0.98687990 Axis point 157.34041998 128.70985965 0.00000000 Rotation angle (degrees) 130.92072050 Shift along axis -5.30631665 > ui mousemode right ""rotate selected models"" > select add #25 2 models selected > view matrix models > #25,-0.47042,-0.83357,-0.28961,363.38,0.84754,-0.51818,0.11478,76.044,-0.24575,-0.19146,0.95024,72.926 > ui mousemode right ""translate selected models"" > view matrix models > #25,-0.47042,-0.83357,-0.28961,355.09,0.84754,-0.51818,0.11478,66.81,-0.24575,-0.19146,0.95024,74.95 > view matrix models > #25,-0.47042,-0.83357,-0.28961,355.15,0.84754,-0.51818,0.11478,66.803,-0.24575,-0.19146,0.95024,74.561 > fitmap #25 inMap #24 Fit map CS_P4_J255_sharp_flip.mrc in map CS_P4_J176_NU_sharp_flip.mrc using 5116 points correlation = 0.8943, correlation about mean = 0.6059, overlap = 8709 steps = 84, shift = 8.95, angle = 14.5 degrees Position of CS_P4_J255_sharp_flip.mrc (#25) relative to CS_P4_J176_NU_sharp_flip.mrc (#24) coordinates: Matrix rotation and translation -0.48869161 0.86324945 -0.12641554 102.63693670 -0.86157381 -0.50031742 -0.08586638 328.42188396 -0.13737200 0.06695414 0.98825405 11.50507804 Axis 0.08825319 0.00632731 -0.99607798 Axis point 146.96136624 134.50878130 0.00000000 Rotation angle (degrees) 120.02497766 Shift along axis -0.32389146 > select subtract #25 Nothing selected > save CS_P4_J255_sharp_flip.mrc #25 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J256_003_volume_map_sharp.mrc"" Opened cryosparc_P4_J256_003_volume_map_sharp.mrc as #26, grid size 80,80,80, pixel 3.32, shown at level 1.01, step 1, values float32 > hide #!25 models > hide #!24 models > select add #26 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #26,-0.89385,-0.39986,0.20284,290.33,-0.34063,0.89978,0.2727,28.49,-0.29155,0.17466,-0.94047,242.77 > select subtract #26 Nothing selected > show #!25 models > fitmap #26 inMap #25 Fit map cryosparc_P4_J256_003_volume_map_sharp.mrc in map CS_P4_J255_sharp_flip.mrc using 5120 points correlation = 0.5232, correlation about mean = 0.0553, overlap = 3214 steps = 120, shift = 25.3, angle = 15.3 degrees Position of cryosparc_P4_J256_003_volume_map_sharp.mrc (#26) relative to CS_P4_J255_sharp_flip.mrc (#25) coordinates: Matrix rotation and translation -0.15531756 0.84438274 0.51273214 -19.64184672 0.98713928 0.15254692 0.04780678 -29.86548711 -0.03784849 0.51356326 -0.85721658 167.46829582 Axis 0.63355180 0.74893504 0.19418658 Axis point 24.16142457 0.00000000 89.91884511 Rotation angle (degrees) 158.43381860 Shift along axis -2.29134077 > select add #26 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #26,-0.87857,-0.47692,-0.025855,314.85,-0.44818,0.80449,0.38978,38.161,-0.16509,0.35404,-0.92054,233.61 > ui mousemode right ""rotate selected models"" > view matrix models > #26,-0.93629,-0.25688,0.23952,260.92,-0.23661,0.96532,0.11035,19.606,-0.25956,0.046645,-0.9646,294.56 > ui mousemode right ""translate selected models"" > view matrix models > #26,-0.93629,-0.25688,0.23952,186.31,-0.23661,0.96532,0.11035,26.555,-0.25956,0.046645,-0.9646,285.53 > select subtract #26 Nothing selected > volume flip #26 Opened cryosparc_P4_J256_003_volume_map_sharp.mrc z flip as #27, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #26 > select add #27 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #27,-0.91261,-0.40844,0.017647,236.5,0.22697,-0.47029,0.85283,55.691,-0.34003,0.78231,0.5219,-22.328 > view matrix models > #27,-0.9144,-0.40478,0.0045882,238.13,0.22235,-0.49276,0.84128,61.136,-0.33827,0.77029,0.54058,-23.608 > view matrix models > #27,-0.50015,0.79795,-0.33634,63.369,-0.80597,-0.57099,-0.15615,357.35,-0.31664,0.19298,0.92871,-2.4372 > ui mousemode right ""translate selected models"" > view matrix models > #27,-0.50015,0.79795,-0.33634,139.66,-0.80597,-0.57099,-0.15615,346.55,-0.31664,0.19298,0.92871,33.757 > fitmap #27 inMap #25 Fit map cryosparc_P4_J256_003_volume_map_sharp.mrc z flip in map CS_P4_J255_sharp_flip.mrc using 5120 points correlation = 0.5523, correlation about mean = 0.08213, overlap = 3668 steps = 72, shift = 2.85, angle = 5.49 degrees Position of cryosparc_P4_J256_003_volume_map_sharp.mrc z flip (#27) relative to CS_P4_J255_sharp_flip.mrc (#25) coordinates: Matrix rotation and translation -0.50078193 -0.83716343 -0.21994286 353.70374510 0.81104417 -0.54259583 0.21862553 68.19134780 -0.30236538 -0.06889966 0.95069870 54.62167416 Axis -0.17164375 0.04920372 0.98392958 Axis point 162.79794553 129.91438640 0.00000000 Rotation angle (degrees) 123.11624986 Shift along axis -3.61188964 > view matrix models > #27,-0.56613,0.75777,-0.32448,155.66,-0.74832,-0.63753,-0.18323,351.66,-0.34571,0.13908,0.92798,47.028 > ui mousemode right ""rotate selected models"" > view matrix models > #27,0.96274,0.27031,-0.0085132,-30.789,-0.27044,0.96237,-0.026732,40.459,0.00096683,0.028039,0.99961,4.8234 > fitmap #27 inMap #25 Fit map cryosparc_P4_J256_003_volume_map_sharp.mrc z flip in map CS_P4_J255_sharp_flip.mrc using 5120 points correlation = 0.9111, correlation about mean = 0.5876, overlap = 9195 steps = 60, shift = 4.49, angle = 4.9 degrees Position of cryosparc_P4_J256_003_volume_map_sharp.mrc z flip (#27) relative to CS_P4_J255_sharp_flip.mrc (#25) coordinates: Matrix rotation and translation -0.48877401 0.86149397 -0.13757950 104.57166396 -0.86119668 -0.50165763 -0.08173068 327.97179743 -0.13942829 0.07853517 0.98711295 10.19538079 Axis 0.09263223 0.00106859 -0.99569982 Axis point 147.63593381 133.73777093 0.00000000 Rotation angle (degrees) 120.10984192 Shift along axis -0.11436514 > select subtract #27 Nothing selected > hide #!25 models > rename #27 CS_P4_J256_sharp_flip id #26 > save CS_P4_J256_sharp_flip.mrc #26 > show #!25 models > hide #!25 models > hide #!26 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J257_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J257_002_volume_map_sharp.mrc as #27, grid size 80,80,80, pixel 3.32, shown at level 0.915, step 1, values float32 > select add #27 2 models selected > show #!26 models > view matrix models > #27,0.43348,0.88304,0.17982,-64.533,0.89699,-0.44198,0.0081618,72.887,0.086685,0.15776,-0.98367,205.49 > hide #!26 models > select subtract #27 Nothing selected > volume flip #27 Opened cryosparc_P4_J257_002_volume_map_sharp.mrc z flip as #28, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #27 > select add #28 2 models selected > show #!26 models > view matrix models > #28,0.0384,0.0015757,0.99926,-5.8546,0.92609,-0.37568,-0.034996,65.933,0.37535,0.92675,-0.015886,-77.078 > view matrix models > #28,0.75378,0.65514,-0.051086,-44.642,-0.54582,0.58092,-0.60384,218.55,-0.36592,0.48304,0.79547,-29.499 > view matrix models > #28,0.93053,0.32568,-0.16747,-7.3436,-0.34314,0.93516,-0.087963,68.823,0.12796,0.13932,0.98195,-76.969 > ui mousemode right ""translate selected models"" > view matrix models > #28,0.93053,0.32568,-0.16747,-12.031,-0.34314,0.93516,-0.087963,69.72,0.12796,0.13932,0.98195,-23.264 > select subtract #28 Nothing selected > fitmap #28 inMap #26 Fit map cryosparc_P4_J257_002_volume_map_sharp.mrc z flip in map CS_P4_J256_sharp_flip.mrc using 5113 points correlation = 0.961, correlation about mean = 0.8355, overlap = 1.813e+04 steps = 76, shift = 3.44, angle = 10.7 degrees Position of cryosparc_P4_J257_002_volume_map_sharp.mrc z flip (#28) relative to CS_P4_J256_sharp_flip.mrc (#26) coordinates: Matrix rotation and translation 0.99983973 0.00266136 0.01770477 -3.60430289 -0.00275366 0.99998275 0.00519130 -0.72993632 -0.01769065 -0.00523922 0.99982979 3.00234542 Axis -0.27967225 0.94905354 -0.14519233 Axis point 166.73187411 0.00000000 206.99324341 Rotation angle (degrees) 1.06849905 Shift along axis -0.12064266 > rename #28 CS_P4_J257_sharp_flip id #27 > save CS_P4_J257_sharp_flip.mrc #27 > hide #!26 models > hide #!27 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J258_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J258_002_volume_map_sharp.mrc as #28, grid size 80,80,80, pixel 3.32, shown at level 0.533, step 1, values float32 > select add #28 2 models selected > show #!27 models > view matrix models #28,1,0,0,2.9293,0,1,0,12.799,0,0,1,30.196 > ui mousemode right ""rotate selected models"" > view matrix models > #28,-0.94564,-0.32466,0.018849,316.84,-0.32175,0.94244,0.090998,54.708,-0.047307,0.079987,-0.99567,265.03 > select up 56 models selected > select up 56 models selected > select down 2 models selected > select down 2 models selected > select subtract #28 Nothing selected > hide #!27 models > volume flip #28 Opened cryosparc_P4_J258_002_volume_map_sharp.mrc z flip as #29, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #28 > select add #29 2 models selected > view matrix models > #29,0.95822,0.27409,-0.081793,-16.892,-0.27702,0.96049,-0.026814,62.796,0.071212,0.048352,0.99629,-31.428 > show #!27 models > select subtract #29 Nothing selected > fitmap #29 inMap #27 Fit map cryosparc_P4_J258_002_volume_map_sharp.mrc z flip in map CS_P4_J257_sharp_flip.mrc using 5117 points correlation = 0.4043, correlation about mean = 0.1105, overlap = 1145 steps = 104, shift = 9.56, angle = 9.45 degrees Position of cryosparc_P4_J258_002_volume_map_sharp.mrc z flip (#29) relative to CS_P4_J257_sharp_flip.mrc (#27) coordinates: Matrix rotation and translation 0.98218261 0.18784329 -0.00567361 -27.82492616 -0.18685004 0.97932905 0.07747035 28.59524537 0.02010861 -0.07502992 0.99697851 -24.36927466 Axis -0.37621012 -0.06360338 -0.92434872 Axis point 152.56947582 100.16313614 0.00000000 Rotation angle (degrees) 11.69370116 Shift along axis 31.17497259 > select add #29 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #29,0.91472,0.40193,-0.041674,-52.044,-0.39883,0.91458,0.066882,60.074,0.064997,-0.044558,0.99689,0.70588 > view matrix models > #29,0.91472,0.40193,-0.041674,-39.705,-0.39883,0.91458,0.066882,54.066,0.064997,-0.044558,0.99689,6.2725 > fitmap #29 inMap #27 Fit map cryosparc_P4_J258_002_volume_map_sharp.mrc z flip in map CS_P4_J257_sharp_flip.mrc using 5117 points correlation = 0.8335, correlation about mean = 0.5457, overlap = 5135 steps = 64, shift = 1.52, angle = 12.1 degrees Position of cryosparc_P4_J258_002_volume_map_sharp.mrc z flip (#29) relative to CS_P4_J257_sharp_flip.mrc (#27) coordinates: Matrix rotation and translation 0.99996433 -0.00752131 -0.00383843 1.74823892 0.00752090 0.99997170 -0.00012121 -0.88867123 0.00383923 0.00009234 0.99999262 -0.68815928 Axis 0.01264381 -0.45457780 0.89061729 Axis point 130.32470586 232.13443622 0.00000000 Rotation angle (degrees) 0.48385831 Shift along axis -0.18681194 > select subtract #29 Nothing selected > rename #29 CS_P4_J258_sharp_flip id #28 > save CS_P4_J258_sharp_flip.mrc #28 > hide #!27 models > hide #!28 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J259_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J259_002_volume_map_sharp.mrc as #29, grid size 80,80,80, pixel 3.32, shown at level 0.567, step 1, values float32 > select add #29 2 models selected > show #!28 models > view matrix models #29,1,0,0,-4.0284,0,1,0,3.9973,0,0,1,26.374 > ui mousemode right ""rotate selected models"" > view matrix models > #29,0.37373,0.91624,0.14434,-63.019,0.92743,-0.36674,-0.073343,74.867,-0.014266,0.16128,-0.98681,258.72 > view matrix models > #29,0.2129,0.93735,0.27578,-60.698,0.97539,-0.1873,-0.11636,49.108,-0.057419,0.29377,-0.95415,242.23 > hide #!28 models > select subtract #29 Nothing selected > volume flip #29 Opened cryosparc_P4_J259_002_volume_map_sharp.mrc z flip as #30, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #29 > select add #30 2 models selected > show #!28 models > view matrix models > #30,0.90176,0.31537,-0.29559,8.3185,-0.32745,0.94483,0.0091223,54.046,0.28216,0.088565,0.95527,-34.506 > select subtract #30 Nothing selected > fitmap #30 inMap #28 Fit map cryosparc_P4_J259_002_volume_map_sharp.mrc z flip in map CS_P4_J258_sharp_flip.mrc using 5112 points correlation = 0.9666, correlation about mean = 0.6628, overlap = 3020 steps = 80, shift = 5.99, angle = 15.1 degrees Position of cryosparc_P4_J259_002_volume_map_sharp.mrc z flip (#30) relative to CS_P4_J258_sharp_flip.mrc (#28) coordinates: Matrix rotation and translation 0.99996699 0.00262374 -0.00768921 0.94371527 -0.00261765 0.99999625 0.00080251 0.08556771 0.00769129 -0.00078235 0.99997011 -0.47262490 Axis -0.09707497 -0.94207663 -0.32104217 Axis point 62.77947672 0.00000000 122.20423531 Rotation angle (degrees) 0.46771540 Shift along axis -0.02048995 > rename #30 CS_P4_J259_sharp_flip id #29 > save CS_P4_J259_sharp_flip.mrc #29 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260502_SA-F_B1_workflow.cxs"" > hide #!29 models > hide #!28 models > show #!25 models > color #25 #FCEDFF > hide #!25 models > show #!28 models > color #28 #FCEDFF > hide #!28 models > show #!29 models > color #29 #FCEDFF > hide #!29 models > show #!29 models > show #!26 models > hide #!29 models > color #26 #99BFE5 > hide #!26 models > show #!27 models > color #27 #99BFE5 > view P1 > hide #!27 models > show #!25 models > ui mousemode right ""translate selected models"" > ui mousemode right translate > view P1 > save CS_P4_J255_NU_sharp.png supersample 3 transparentBackground true > hide #!25 models > show #!26 models > volume #26 level 1.012 > save CS_P4_J256_NU_sharp.png supersample 3 transparentBackground true > hide #!26 models > show #!27 models > save CS_P4_J257_NU_sharp.png supersample 3 transparentBackground true > hide #!27 models > show #!28 models > save CS_P4_J258_NU_sharp.png supersample 3 transparentBackground true > hide #!28 models > show #!29 models > save CS_P4_J259_NU_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260502_SA-F_B1_workflow.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J285_006_volume_map_sharp.mrc"" Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.0363, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J267_008_volume_map_sharp.mrc"" Opened cryosparc_P4_J267_008_volume_map_sharp.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.0747, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J277_008_volume_map_sharp.mrc"" Opened cryosparc_P4_J277_008_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0762, step 2, values float32 > hide #!29 models > hide #!30 models > hide #!31 models > show #!31 models > hide #!32 models > show #!30 models > close #30 > show #!27 models > select add #31 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #31,-0.90396,0.26529,0.33537,196.37,0.29187,0.95597,0.030503,-41.724,-0.31251,0.12546,-0.94159,315.51 > hide #!27 models > view matrix models > #31,-0.95736,-0.095902,0.27253,266.49,-0.06692,0.99125,0.11374,-5.5307,-0.28105,0.090649,-0.9554,317.94 > show #!29 models > hide #!29 models > select subtract #31 Nothing selected > close #32 > volume flip #31 Opened cryosparc_P4_J267_008_volume_map_sharp.mrc z flip as #30, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #30 > show #!31 models > select add #31 2 models selected > show #!27 models > ui mousemode right ""translate selected models"" > view matrix models > #31,-0.95736,-0.095902,0.27253,258.1,-0.06692,0.99125,0.11374,14.401,-0.28105,0.090649,-0.9554,295.97 > ui mousemode right ""rotate selected models"" > view matrix models > #31,0.57983,0.79903,0.15922,-85.975,0.81408,-0.57604,-0.073785,139.64,0.032763,0.1724,-0.98448,241.38 > ui mousemode right ""translate selected models"" > view matrix models > #31,0.57983,0.79903,0.15922,-74.26,0.81408,-0.57604,-0.073785,114.14,0.032763,0.1724,-0.98448,243.66 > ui mousemode right ""rotate selected models"" > view matrix models > #31,0.38773,0.91358,0.12259,-56.869,0.92165,-0.3821,-0.067497,68.753,-0.014823,0.13915,-0.99016,256.48 > ui mousemode right ""translate selected models"" > view matrix models > #31,0.38773,0.91358,0.12259,-59.17,0.92165,-0.3821,-0.067497,73.776,-0.014823,0.13915,-0.99016,255.81 > fitmap #31 inMap #27 Fit map cryosparc_P4_J267_008_volume_map_sharp.mrc in map CS_P4_J257_sharp_flip.mrc using 40948 points correlation = 0.4368, correlation about mean = 0.04808, overlap = 2838 steps = 84, shift = 6.03, angle = 16 degrees Position of cryosparc_P4_J267_008_volume_map_sharp.mrc (#31) relative to CS_P4_J257_sharp_flip.mrc (#27) coordinates: Matrix rotation and translation -0.09805932 0.98945486 0.10659935 2.84911711 0.99008140 0.10782511 -0.09006967 -2.59568012 -0.10061396 0.09670986 -0.99021412 262.50076525 Axis 0.66953234 0.74277951 0.00224590 Axis point 14.97851108 -0.00000000 131.13786872 Rotation angle (degrees) 171.98194915 Shift along axis 0.56910865 > select subtract #31 Nothing selected > hide #!31 models > hide #!27 models > show #!31 models > close #31 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J267_008_volume_map_sharp.mrc"" Opened cryosparc_P4_J267_008_volume_map_sharp.mrc as #30, grid size 320,320,320, pixel 0.831, shown at level 0.0747, step 2, values float32 > select add #30 2 models selected > show #!27 models > ui mousemode right ""rotate selected models"" > view matrix models > #30,0.59059,-0.80637,-0.031153,183.8,-0.80688,-0.59066,-0.008015,354.56,-0.011937,0.02987,-0.99948,293.1 > ui mousemode right ""translate selected models"" > view matrix models > #30,0.59059,-0.80637,-0.031153,187.84,-0.80688,-0.59066,-0.008015,342.67,-0.011937,0.02987,-0.99948,267.57 > hide #!27 models > show #!27 models > hide #!30 models > hide #!27 models > show #!30 models > volume flip #30 Opened cryosparc_P4_J267_008_volume_map_sharp.mrc z flip as #31, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > select subtract #30 Nothing selected > close #30 > select add #31 2 models selected > show #!27 models > view matrix models > #31,0.59059,-0.80637,-0.031153,181.08,-0.80688,-0.59066,-0.008015,342.68,-0.011937,0.02987,-0.99948,285.6 > ui mousemode right ""rotate selected models"" > view matrix models > #31,0.49825,-0.85813,0.12394,182.63,-0.032454,0.12438,0.9917,19.314,-0.86642,-0.49814,0.034125,354.11 > view matrix models > #31,-0.47795,-0.87619,-0.061991,343.39,0.85267,-0.47976,0.20686,70.492,-0.21099,0.046011,0.9764,77.316 > ui mousemode right ""translate selected models"" > view matrix models > #31,-0.47795,-0.87619,-0.061991,322.39,0.85267,-0.47976,0.20686,71.691,-0.21099,0.046011,0.9764,36.515 > view matrix models > #31,-0.47795,-0.87619,-0.061991,329.78,0.85267,-0.47976,0.20686,58.248,-0.21099,0.046011,0.9764,36.244 > fitmap #31 inMap #27 Fit map cryosparc_P4_J267_008_volume_map_sharp.mrc z flip in map CS_P4_J257_sharp_flip.mrc using 327854 points correlation = 0.6967, correlation about mean = 0.2684, overlap = 4.49e+04 steps = 92, shift = 8.63, angle = 16.2 degrees Position of cryosparc_P4_J267_008_volume_map_sharp.mrc z flip (#31) relative to CS_P4_J257_sharp_flip.mrc (#27) coordinates: Matrix rotation and translation -0.48810574 -0.85845883 -0.15748400 338.09346066 0.86132304 -0.50293557 0.07196129 74.97027819 -0.14098011 -0.10051988 0.98489611 32.48936744 Axis -0.09978729 -0.00954816 0.99496298 Axis point 149.01931346 135.27108975 0.00000000 Rotation angle (degrees) 120.20349080 Shift along axis -2.12754240 > select subtract #31 Nothing selected > volume #27 level 1.164 > volume #31 level 0.1055 > hide #!27 models > volume #31 level 0.1343 > color #31 #99BFE5 > rename #31 CS_P4_J267_sharp_flip id #30 > save CS_P4_J267_sharp_flip.mrc #30 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J277_008_volume_map_sharp.mrc"" Opened cryosparc_P4_J277_008_volume_map_sharp.mrc as #31, grid size 320,320,320, pixel 0.831, shown at level 0.0762, step 2, values float32 > hide #!30 models > select add #31 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #31,0.50169,-0.77701,0.38022,112.38,-0.8444,-0.53533,0.020189,301.01,0.18786,-0.33119,-0.92467,273.22 > view matrix models > #31,0.77218,-0.62718,0.10187,94.664,-0.63536,-0.764,0.11236,288.83,0.0073633,-0.15149,-0.98843,283.82 > volume flip #31 Opened cryosparc_P4_J277_008_volume_map_sharp.mrc z flip as #32, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #31 > select add #32 2 models selected > show #!30 models > view matrix models > #32,0.90608,0.27127,-0.3247,15.596,-0.28323,0.95899,0.010829,28.44,0.31432,0.082155,0.94575,-47.16 > view matrix models > #32,0.99239,-0.018676,-0.12173,15.559,0.019459,0.9998,0.0052468,-15.401,0.1216,-0.0075755,0.99255,-16.612 > ui mousemode right ""translate selected models"" > view matrix models > #32,0.99239,-0.018676,-0.12173,21.14,0.019459,0.9998,0.0052468,-2.6957,0.1216,-0.0075755,0.99255,-9.4459 > fitmap #32 inMap #30 Fit map cryosparc_P4_J277_008_volume_map_sharp.mrc z flip in map CS_P4_J267_sharp_flip.mrc using 327711 points correlation = 0.7196, correlation about mean = 0.3385, overlap = 5671 steps = 204, shift = 3.68, angle = 13.7 degrees Position of cryosparc_P4_J277_008_volume_map_sharp.mrc z flip (#32) relative to CS_P4_J267_sharp_flip.mrc (#30) coordinates: Matrix rotation and translation -0.48144357 0.86501463 -0.14128627 103.86408789 -0.86432037 -0.49531179 -0.08727288 328.52215562 -0.14547307 0.08009963 0.98611442 10.75546195 Axis 0.09633390 0.00240978 -0.99534616 Axis point 148.32654443 133.96556119 0.00000000 Rotation angle (degrees) 119.69088439 Shift along axis 0.09189113 > select subtract #32 Nothing selected > volume #32 level 0.1306 > hide #!30 models > volume #32 level 0.1432 > color #32 #99BFE5 > rename #32 CS_P4_J277_sharp_flip id #31 > save CS_P4_J277_sharp_flip.mrc #31 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J285_006_volume_map_sharp.mrc"" Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0363, step 2, values float32 > hide #!31 models > select add #32 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #32,0.30706,0.95043,0.049005,-33.318,0.9497,-0.30268,-0.080397,47.411,-0.061579,0.071226,-0.99556,261.24 > volume flip #32 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #33, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > show #!31 models > show #!32 models > view matrix models > #32,0.19586,0.82677,-0.52734,72.951,0.95192,-0.28947,-0.10029,48.053,-0.23556,-0.48235,-0.84371,334.74 > view matrix models > #32,0.038463,0.98737,0.15371,-15.568,0.97818,-0.0057722,-0.20769,22.74,-0.20418,0.15835,-0.96604,265.55 > close #32 > select add #33 2 models selected > view matrix models > #33,-0.36526,-0.91739,-0.15805,324.89,0.9276,-0.34439,-0.14472,64.223,0.078335,-0.19947,0.97677,17.619 > view matrix models > #33,-0.3296,-0.92737,-0.17708,323.89,0.91639,-0.35937,0.17633,25.386,-0.22716,-0.10416,0.96827,47.503 > select subtract #33 Nothing selected > fitmap #33 inMap #31 Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map CS_P4_J277_sharp_flip.mrc using 327344 points correlation = 0.3754, correlation about mean = 0.04431, overlap = 1099 steps = 64, shift = 4.4, angle = 1.24 degrees Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative to CS_P4_J277_sharp_flip.mrc (#31) coordinates: Matrix rotation and translation -0.52307807 -0.83656982 -0.16291178 338.77635518 0.81824450 -0.54640858 0.17864376 66.60900444 -0.23846438 -0.03985703 0.97033300 35.38091339 Axis -0.13076939 0.04521708 0.99038113 Axis point 153.51682890 124.48577590 0.00000000 Rotation angle (degrees) 123.33798629 Shift along axis -6.24912375 > volume #33 level 0.05666 > select add #33 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #33,-0.32295,-0.92807,-0.18543,326.53,0.9135,-0.3569,0.19529,26.322,-0.24742,-0.10632,0.96306,60.406 > fitmap #33 inMap #31 Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map CS_P4_J277_sharp_flip.mrc using 194771 points correlation = 0.7316, correlation about mean = 0.2783, overlap = 2429 steps = 104, shift = 3.72, angle = 6.69 degrees Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative to CS_P4_J277_sharp_flip.mrc (#31) coordinates: Matrix rotation and translation -0.48329817 -0.86312458 -0.14641999 335.54076959 0.86340511 -0.49758655 0.08330200 72.08568886 -0.14475663 -0.08616006 0.98570885 33.43360614 Axis -0.09768239 -0.00095880 0.99521718 Axis point 148.43445219 133.71191357 0.00000000 Rotation angle (degrees) 119.84054702 Shift along axis 0.42815717 > select subtract #33 Nothing selected > select add #33 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #33,-0.6364,0.75107,-0.17577,140.89,-0.74512,-0.6575,-0.11171,345.32,-0.19948,0.059876,0.97807,29.849 > ui mousemode right ""translate selected models"" > view matrix models > #33,-0.6364,0.75107,-0.17577,136.82,-0.74512,-0.6575,-0.11171,338.86,-0.19948,0.059876,0.97807,29.687 > ui mousemode right ""rotate selected models"" > view matrix models > #33,-0.73358,0.64738,-0.20678,168.84,-0.63708,-0.76101,-0.12246,339.46,-0.23664,0.041901,0.97069,38.344 > fitmap #33 inMap #31 Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map CS_P4_J277_sharp_flip.mrc using 194771 points correlation = 0.4346, correlation about mean = 0.05784, overlap = 1046 steps = 96, shift = 4.05, angle = 4.16 degrees Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative to CS_P4_J277_sharp_flip.mrc (#31) coordinates: Matrix rotation and translation -0.58502424 0.80932802 -0.05229508 107.72395607 -0.80221021 -0.58694418 -0.10934029 332.49911712 -0.11918646 -0.02201508 0.99262777 22.68232922 Axis 0.05406170 0.04141143 -0.99767852 Axis point 139.16943260 139.24984383 0.00000000 Rotation angle (degrees) 126.13361686 Shift along axis -3.03667024 > ui mousemode right ""translate selected models"" > view matrix models > #33,-0.7311,0.66788,-0.13939,159.58,-0.65889,-0.74418,-0.10984,339.55,-0.17709,0.011538,0.98413,33.11 > fitmap #33 inMap #31 Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map CS_P4_J277_sharp_flip.mrc using 194771 points correlation = 0.7261, correlation about mean = 0.2429, overlap = 2435 steps = 148, shift = 3.57, angle = 8.91 degrees Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative to CS_P4_J277_sharp_flip.mrc (#31) coordinates: Matrix rotation and translation -0.47691102 0.86730315 -0.14262219 103.16958211 -0.86637561 -0.49120809 -0.09004393 328.47939238 -0.14815256 0.08062145 0.98567285 11.48812128 Axis 0.09796714 0.00317460 -0.99518459 Axis point 148.54824739 133.97305983 0.00000000 Rotation angle (degrees) 119.42100612 Shift along axis -0.28278057 > ui mousemode right ""rotate selected models"" > view matrix models > #33,0.98687,0.16137,0.0076046,-28.356,-0.15803,0.97406,-0.16197,41.243,-0.033544,0.15864,0.98677,-7.5792 > ui mousemode right ""translate selected models"" > view matrix models > #33,0.98687,0.16137,0.0076046,-22.398,-0.15803,0.97406,-0.16197,51.235,-0.033544,0.15864,0.98677,-4.7399 > fitmap #33 inMap #31 Fit map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip in map CS_P4_J277_sharp_flip.mrc using 194771 points correlation = 0.9896, correlation about mean = 0.9159, overlap = 4214 steps = 120, shift = 4.17, angle = 9.65 degrees Position of cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#33) relative to CS_P4_J277_sharp_flip.mrc (#31) coordinates: Matrix rotation and translation 0.99997973 -0.00439362 0.00460748 -0.02530815 0.00439161 0.99999024 0.00044636 -0.51759472 -0.00460939 -0.00042611 0.99998927 1.01725436 Axis -0.06835965 0.72216012 0.68833983 Axis point 171.68283436 0.00000000 1.37920014 Rotation angle (degrees) 0.36563312 Shift along axis 0.32816049 > select subtract #33 Nothing selected > hide #!31 models > show #!31 models > hide #!31 models > volume #33 level 0.06481 > color #33 #99BFE5 > view P1 > rename #33 CS_P4_J285_sharp_flip id #32 > save CS_P4_J285_sharp_flip.mrc #32 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260502_SA-F_B1_workflow.cxs"" > save CS_P4_J285_NU_sharp.png supersample 3 transparentBackground true > hide #!32 models > show #!31 models > save CS_P4_J277_NU_sharp.png supersample 3 transparentBackground true > hide #!31 models > show #!30 models > save CS_P4_J267_NU_sharp.png supersample 3 transparentBackground true > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J282_005_volume_map_sharp.mrc"" Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32 > select add #33 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #33,0.77382,-0.58736,0.23709,68.017,-0.6199,-0.77915,0.092993,287.71,0.13011,-0.21893,-0.96703,293.89 > volume flip sel Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #34, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > select subtract #33 Nothing selected > select add #34 2 models selected > view matrix models > #34,0.96024,0.18105,-0.2125,4.9844,-0.18441,0.98284,0.0040821,22.146,0.20959,0.035266,0.97715,4.1522 > volume #34 level 0.06153 > ui mousemode right ""translate selected models"" > view matrix models > #34,0.96024,0.18105,-0.2125,5.3992,-0.18441,0.98284,0.0040821,24.944,0.20959,0.035266,0.97715,-19.851 > fitmap #34 inMap #30 Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map CS_P4_J267_sharp_flip.mrc using 179913 points correlation = 0.7668, correlation about mean = 0.2691, overlap = 2384 steps = 132, shift = 4.76, angle = 10.2 degrees Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#34) relative to CS_P4_J267_sharp_flip.mrc (#30) coordinates: Matrix rotation and translation -0.47859383 0.86460690 -0.15297990 105.65226772 -0.86128787 -0.49615211 -0.10961884 331.90892973 -0.17067851 0.07929683 0.98213077 14.98614385 Axis 0.10880400 0.01019333 -0.99401096 Axis point 150.51207819 135.19673705 0.00000000 Rotation angle (degrees) 119.75601097 Shift along axis -0.01774616 > select subtract #34 Nothing selected > select add #34 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #34,-0.29858,-0.92833,-0.22151,340.08,0.93935,-0.32688,0.10377,36.917,-0.16874,-0.17709,0.96962,60.484 > fitmap #34 inMap #30 Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map CS_P4_J267_sharp_flip.mrc using 179913 points correlation = 0.4184, correlation about mean = 0.03499, overlap = 815.8 steps = 72, shift = 3.19, angle = 2.56 degrees Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#34) relative to CS_P4_J267_sharp_flip.mrc (#30) coordinates: Matrix rotation and translation 0.99975679 -0.00914856 -0.02006678 -0.29483780 0.00937915 0.99989072 0.01142689 -12.23865962 0.01996005 -0.01161232 0.99973334 -0.12571505 Axis -0.46299067 -0.80436995 0.37232865 Axis point 194.44052306 0.00000000 212.15518455 Rotation angle (degrees) 1.42571524 Shift along axis 9.93410983 > ui mousemode right ""translate selected models"" > view matrix models > #34,-0.29149,-0.93644,-0.19523,323.34,0.9479,-0.31019,0.07257,35.755,-0.12852,-0.16391,0.97807,48.671 > fitmap #34 inMap #30 Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map CS_P4_J267_sharp_flip.mrc using 179913 points correlation = 0.9696, correlation about mean = 0.7683, overlap = 3705 steps = 76, shift = 2.39, angle = 2.68 degrees Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#34) relative to CS_P4_J267_sharp_flip.mrc (#30) coordinates: Matrix rotation and translation 0.99970034 -0.00006024 0.02447927 -4.11138943 0.00004629 0.99999984 0.00057062 0.05899118 -0.02447930 -0.00056932 0.99970018 3.40337319 Axis -0.02327752 0.99972667 0.00217546 Axis point 136.94050248 0.00000000 169.47617625 Rotation angle (degrees) 1.40308329 Shift along axis 0.16208189 > select subtract #34 Nothing selected > hide #!30 models > show #!32 models > hide #!31 models > volume #34 level 0.06805 > hide #!32 models > view P1 > close #33 > rename #34 CS_P4_J282_sharp_flip id #33 > save CS_P4_J282_sharp_flip.mrc #33 > view P1 > save CS_P4_J282_NU_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260502_SA-F_B1_workflow1.cxs"" > color #33 #99BFE5 > save CS_P4_J282_NU_sharp1.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260502_SA-F_B1_workflow1.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J287_map_locres.mrc"" Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 9.77, step 2, values float32 > rename #34 cryosparc_P4_J287_map_locres_forJ282 > select add #34 2 models selected > view matrix models #34,1,0,0,-1.0935,0,1,0,0.90366,0,0,1,6.3532 > ui mousemode right ""rotate selected models"" > view matrix models > #34,0.41458,0.88648,0.20563,-71.892,0.90978,-0.4089,-0.07146,80.866,0.020734,0.2167,-0.97602,247.42 > view matrix models > #34,0.40248,0.89866,0.17442,-67.589,0.91533,-0.39227,-0.091056,80.514,-0.013407,0.1963,-0.98045,255.56 > view matrix models > #34,0.3547,0.92587,0.13022,-58.659,0.93218,-0.33944,-0.12576,75.687,-0.072238,0.166,-0.98348,268.27 > fitmap #34 inMap #33 Fit map cryosparc_P4_J287_map_locres_forJ282 in map CS_P4_J282_sharp_flip.mrc using 40893 points correlation = 0.2997, correlation about mean = 0.02148, overlap = 2955 steps = 140, shift = 9.61, angle = 2.61 degrees Position of cryosparc_P4_J287_map_locres_forJ282 (#34) relative to CS_P4_J282_sharp_flip.mrc (#33) coordinates: Matrix rotation and translation 0.77162333 -0.63598985 0.01069393 118.29154644 -0.63440309 -0.76826072 0.08548800 317.77796206 -0.04615378 -0.07274879 -0.99628182 298.10083492 Axis -0.94106809 0.33808548 0.00943679 Axis point 0.00000000 186.80747823 142.52542945 Rotation angle (degrees) 175.17728056 Shift along axis -1.07117046 > volume #34 level 6.762 > view matrix models > #34,0.42433,0.90126,0.087581,-65.663,0.89997,-0.40908,-0.15069,88.731,-0.099987,0.14276,-0.98469,281 > ui mousemode right ""translate selected models"" > view matrix models > #34,0.42433,0.90126,0.087581,-62.736,0.89997,-0.40908,-0.15069,86.303,-0.099987,0.14276,-0.98469,272.65 > view matrix models > #34,0.42433,0.90126,0.087581,-62.591,0.89997,-0.40908,-0.15069,86.167,-0.099987,0.14276,-0.98469,272.2 > volume #34 level 6.762 > volume #34 level 6.47 > ui tool show ""Surface Color"" > color sample #33.1 map #34 palette #ff0000:#ffffff:#0000ff outsideColor > #808080 Map values for surface ""surface"": minimum 0, mean 4.349, maximum 40.76 > select subtract #34 Nothing selected > hide #!34 models > key red-white-blue :0.0 :20.4 :40.8 showTool true > ui mousemode right ""color key"" > key red-white-blue :0.0 :20.4 :40.8 white: > key red:0.0 white:20.4 blue:40.8 white: white: > key red:0.0 white:20.4 blue:40.8 white: > key red-white-blue :0.0 :20.4 :40.8 > key red-white-blue :0 :2 :4 showTool true > ui mousemode right ""color key"" > key red-white-blue :0 :2 :4 white: > key red:0 white:2 blue:4 white: white: > color single #33.1 > color sample #33.1 map #34 palette 0,#ff0000:2,#ffffff:4,#0000ff > outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.349, maximum 40.76 > key red-white-blue :0 :2 :4 showTool true > ui mousemode right ""color key"" > key red-white-blue :0 :2 :4 showTool true > key red-white-blue :0 :2 :4 white: > key red:0 white:2 blue:4 white: white: > key red:0 white:2 blue:4 white: white:0 > key red:0 white:2 blue:4 white:1 white:0 > key red:0 white:2 blue:2 white:1 white:0 > key red:0 white:3 blue:2 white:1 white:0 > key red:4 white:3 blue:2 white:1 white:0 > key gnbu :4 :3 :2 :1 :0 > key esmfold :4 :3 :2 :1 :0 > key dark2-5 :4 :3 :2 :1 :0 > key pastel1-5 :4 :3 :2 :1 :0 > key blues :4 :3 :2 :1 :0 > key accent-5 :4 :3 :2 :1 :0 > color sample #33.1 map #34 palette 0,#ff0000:2,#ffffff:4,#0000ff > outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.349, maximum 40.76 > color sample #33.1 map #34 palette 0,#ff0000:2,#ffffff:4,#0000ff > outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.349, maximum 40.76 > color sample #33.1 map #34 palette 0,#0000ff:2,#7f7fff:4,#ffffff > outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.349, maximum 40.76 > key blue:0 #7f7fff:2 white:4 showTool true > ui mousemode right ""color key"" > key blue:0 #7f7fff:2 white:4 showTool true > key blue:0 #7f7fff:2 white:4 white: > key blue:0 #7f7fff:2 white:4 white: white: > color sample #33.1 map #34 palette > 0,#0000ff:1,#7f7fff:2,#ffffff:3,#ff7f7f:4,#ff0000 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.349, maximum 40.76 > key blue:0 #7f7fff:1 white:2 #ff7f7f:3 red:4 showTool true > ui mousemode right ""color key"" > color sample #33.1 map #34 palette > 0,#0000ff:1,#7f7fff:2,#ffffff:3,#ff7f7f:4,#ff0000 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.349, maximum 40.76 > color sample #33.1 map #34 palette > 0,#ff0000:1,#ff7f7f:2,#ffffff:3,#7f7fff:4,#0000ff outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.349, maximum 40.76 > color sample #33.1 map #34 palette > 0,#ff0000:2,#ff7f7f:4,#ffffff:5,#7f7fff:8,#0000ff outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.349, maximum 40.76 > volume #33 level 0.08574 > key red:0 #ff7f7f:2 white:4 #7f7fff:5 blue:8 showTool true > key red:0 #ff7f7f:2 white:4 #7f7fff:6 blue:8 showTool true > color sample #33.1 map #34 palette > 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ff7f7f:8,#ff0000 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.269, maximum 35.43 > color sample #33.1 map #34 palette > 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ff7f7f:8,#fff6c0 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.269, maximum 35.43 > key blue:0 #7f7fff:2 white:4 #ff7f7f:6 #fff6c0:8 showTool true > color sample #33.1 map #34 palette > 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ffad7f:8,#fff6c0 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.269, maximum 35.43 > color sample #33.1 map #34 palette > 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.269, maximum 35.43 > key blue:0 #7f7fff:2 white:4 #ff967f:6 #fff6c0:8 showTool true > color sample #33.1 map #34 palette > 0,#fff6c0:2,#ff967f:4,#ffffff:6,#7f7fff:8,#0000ff outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.269, maximum 35.43 > color sample #33.1 map #34 palette > 0,#0000ff:2,#7f7fff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.269, maximum 35.43 > key blue:0 #7f7fff:2 white:4 #ff967f:6 #fff6c0:8 showTool true > color sample #33.1 map #34 palette > 0,#00a7ff:2,#7f7fff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.269, maximum 35.43 > key #00a7ff:0 #7f7fff:2 white:4 #ff967f:6 #fff6c0:8 showTool true > color sample #33.1 map #34 palette > 0,#00a7ff:2,#d2a5ff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.269, maximum 35.43 > key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260502_SA-F_B1_workflow2.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J288_map_locres.mrc"" Opened cryosparc_P4_J288_map_locres.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 8.93, step 2, values float32 > hide #35 models > show #35 models > hide #!36 models > hide #!33 models > show #!33 models > rename #36 cryosparc_P4_J288_map_locres_forJ285 > hide #!33 models > show #!32 models > hide #35 models > show #!36 models > select add #36 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #36,0.54984,-0.77769,0.30476,129.28,-0.81459,-0.57994,-0.010221,331.17,0.18469,-0.24264,-0.95237,263.23 > ui mousemode right ""translate selected models"" > view matrix models > #36,0.54984,-0.77769,0.30476,119.97,-0.81459,-0.57994,-0.010221,318.58,0.18469,-0.24264,-0.95237,280.96 > volume #36 level 6.234 > select subtract #36 Nothing selected > ui tool show ""Surface Color"" > color sample #32.1 map #36 palette > 0,#00a7ff:2,#d2a5ff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > hide #!36 models > show #!33 models > hide #!33 models > show #!33 models > hide #!32 models > show #!32 models > hide #!33 models > key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true > show #!36 models > hide #!36 models > key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 white: > key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 Fetching compressed palette custom from https://www.colourlovers.com/api/palettes?keywords=custom&format=json&numResults=100 Could not find palette custom at COLOURlovers.com using keyword search > color sample #32.1 map #36 palette > 0,#00a7ff:2,#d2a5ff:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true > hide #!32 models > show #35 models > show #!32 models > select add #35 1 model selected > view matrix models #35,1,0,0,-1.208,0,1,0,-1.3654,0,0,1,1.1486 > select subtract #35 Nothing selected > select add #35 1 model selected > select subtract #35 Nothing selected > key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true > ui mousemode right ""color key"" > select add #35 1 model selected > show #35 > view W35 Expected an objects specifier or a view name or a keyword > view #35 No displayed objects specified. > close #35 > key #00a7ff:0 #d2a5ff:2 white:4 #ff967f:6 #fff6c0:8 showTool true > ui mousemode right ""color key"" > hide #!32 models > show #!33 models > hide #!33 models > show #!33 models > hide #!33 models > show #!33 models > volume #33 level 0.06991 > hide #!33 models > show #!32 models > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260502_SA-F_B1_workflow2.cxs"" > color sample #32.1 map #36 palette > 0,#00a7ff:2,#99bfe5:4,#ffffff:6,#ff967f:8,#fff6c0 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > key #00a7ff:0 #99bfe5:2 white:4 #fff6c0:6 #ff967f:8 showTool true > ui mousemode right ""color key"" > color sample #32.1 map #36 palette > 0,#00a7ff:2,#99bfe5:4,#ffffff:6,#fff6c0:8,#ff967f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#d2a5ff:2,#99bfe5:4,#ffffff:6,#fff6c0:8,#ff967f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > key #d2a5ff:0 #99bfe5:2 white:4 #fff6c0:6 #ff967f:8 showTool true > view #35 No objects specified. > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#99bfe5:4,#ffffff:6,#fff6c0:8,#ff967f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > key #e7c4ff:0 #99bfe5:2 white:4 #fff6c0:6 #ff967f:8 showTool true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260502_SA-F_B1_workflow2.cxs"" > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#99bfe5:4,#5da0ff:6,#fff6c0:8,#ff967f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#e0bfe8:4,#99bfe5:6,#fff6c0:8,#ff967f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#e0dee8:4,#99bfe5:6,#fff6c0:8,#ff967f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#e0dee8:4,#99bfe5:6,#fff6c0:8,#ff967f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#6676ed:4,#99bfe5:6,#fff6c0:8,#ff967f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#6676ed:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#99bfe5:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#99bfe5:4,#6676ed:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#99bfe5:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#799bea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#5756ea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#e7c4ff:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#ffdedd:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#ffc9a3:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > color sample #32.1 map #36 palette > 0,#ffb17f:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.33, maximum 41.38 > key #ffb17f:0 #527dea:2 #99bfe5:4 #fff6c0:6 #f4fff3:8 showTool true > ui mousemode right ""color key"" > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260502_SA-F_B1_workflow3.cxs"" > hide #!32 models > show #!33 models > hide #!33 models > show #!32 models > hide #!32 models > show #!33 models > hide #!33 models > show #!32 models > volume #34 step 1 > volume #36 step 1 > show #!36 models > volume flip #36 Opened cryosparc_P4_J288_map_locres_forJ285 z flip as #38, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > hide #37 models > ui mousemode right ""rotate selected models"" > hide #!32 models > show #!32 models > hide #!38 models > show #!38 models > select add #38 2 models selected > view matrix models > #38,-0.22965,0.94651,-0.22667,61.099,-0.95753,-0.26145,-0.12161,309.34,-0.17437,0.18912,0.96635,13.289 > view matrix models > #38,-0.47581,-0.84028,-0.25987,345.82,0.86453,-0.50117,0.037622,69.811,-0.16185,-0.20677,0.96491,66.334 > view matrix models > #38,-0.72836,0.6263,-0.27792,180.88,-0.55109,-0.77649,-0.30556,349.01,-0.40718,-0.069403,0.91071,88.496 > view matrix models > #38,-0.422,0.88275,-0.20657,93.707,-0.7937,-0.46985,-0.38638,351.04,-0.43814,0.0009021,0.89891,84.657 > fitmap #38 inMap #32 Fit map cryosparc_P4_J288_map_locres_forJ285 z flip in map CS_P4_J285_sharp_flip.mrc using 1112104 points correlation = 0.2781, correlation about mean = -0.02765, overlap = 7.665e+04 steps = 172, shift = 16.7, angle = 11.9 degrees Position of cryosparc_P4_J288_map_locres_forJ285 z flip (#38) relative to CS_P4_J285_sharp_flip.mrc (#32) coordinates: Matrix rotation and translation -0.15731459 0.96448973 -0.21215945 50.76791567 -0.83839054 -0.24396591 -0.48742375 323.17714111 -0.52187488 0.10119361 0.84699849 86.68679965 Axis 0.30630695 0.16117090 -0.93818974 Axis point 169.99659509 146.99779714 0.00000000 Rotation angle (degrees) 106.08964492 Shift along axis -13.69134858 > ui mousemode right ""translate selected models"" > view matrix models > #38,-0.29391,0.88572,-0.35933,106.9,-0.78003,-0.43953,-0.4454,363.34,-0.55243,0.14938,0.82006,93.87 > ui mousemode right ""rotate selected models"" > volume #38 level 4.082 > view matrix models > #38,-0.44764,0.81063,-0.37749,140.89,-0.70715,-0.57929,-0.40543,367.19,-0.54732,0.085454,0.83255,100.3 > ui mousemode right ""translate selected models"" [Repeated 1 time(s)] > view matrix models > #38,-0.44764,0.81063,-0.37749,135.23,-0.70715,-0.57929,-0.40543,367.93,-0.54732,0.085454,0.83255,97.332 > view matrix models > #38,-0.44764,0.81063,-0.37749,134.86,-0.70715,-0.57929,-0.40543,366.07,-0.54732,0.085454,0.83255,96.949 > select subtract #38 Nothing selected > hide #!38 models > color sample #32.1 map #38 palette > 0,#ffb17f:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.286, maximum 42.51 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/CS_P4_J282_sharp_flip.mrc"" Opened CS_P4_J282_sharp_flip.mrc as #39, grid size 320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32 > hide #!32 models > close #39 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J282_005_volume_map_sharp.mrc"" Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J287_map_locres.mrc"" Opened cryosparc_P4_J287_map_locres_forJ282 as #39, grid size 320,320,320, pixel 0.831, shown at level 9.77, step 2, values float32 > volume #39 level 4.139 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J287_map_locres.mrc"" Opened cryosparc_P4_J287_map_locres_forJ282 as #40, grid size 320,320,320, pixel 0.831, shown at level 9.77, step 2, values float32 > close #40 > color sample #35.1 map #39 palette > 0,#ffb17f:2,#527dea:4,#99bfe5:6,#fff6c0:8,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.417, maximum 39.82 > hide #!39 models > volume #35 step 1 > volume #35 level 0.06749 > color sample #35.1 map #39 palette > 0,#ffb17f:1,#527dea:2,#99bfe5:3,#fff6c0:4,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 3.044, mean 3.567, maximum 40.68 > color sample #35.1 map #39 palette > 0,#ffb17f:2,#527dea:3,#99bfe5:4,#fff6c0:5,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 3.044, mean 3.567, maximum 40.68 > color sample #35.1 map #39 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 3.044, mean 3.567, maximum 40.68 > close #32 > close #33 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260503_SA-F_B1_workflow.cxs"" > close #39 > close #38 > close #36 > close #35 > show #!34 models > hide #!34 models > close #34 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J282_005_volume_map_sharp.mrc"" Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #32, grid size 320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J285_006_volume_map_sharp.mrc"" Opened cryosparc_P4_J285_006_volume_map_sharp.mrc as #33, grid size 320,320,320, pixel 0.831, shown at level 0.0363, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J287_map_locres.mrc"" Opened cryosparc_P4_J287_map_locres.mrc as #34, grid size 320,320,320, pixel 0.831, shown at level 9.77, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J288_map_locres.mrc"" Opened cryosparc_P4_J288_map_locres.mrc as #35, grid size 320,320,320, pixel 0.831, shown at level 8.93, step 2, values float32 > rename #37 Color key id #36 Expected a keyword > rename #37 Color_key id #36 Cannot change id of 2D overlay models (Color_key #37) > hide #!33 models > hide #!35 models > volume #34 level 6.298 > volume #34 level 3.171 > volume #34 level 3.779 > hide #!34 models > ui tool show ""Surface Color"" No surface chosen for coloring > show #!34 models > hide #!34 models > color sample #32.1 map #34 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.417, maximum 39.82 > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" Could not find palette custom at COLOURlovers.com using keyword search > show #37 models > key pos 0.558738,0.385722 size 0.0255738,0.0868715 > key pos 0.723062,0.0751149 > key pos 0.862303,0.0795068 > key pos 0.846838,0.0779833 > select add #37 1 model selected > key pos 0.819995,0.0796645 > key pos 0.812107,0.0767711 > key pos 0.825223,0.13099 > select subtract #37 Nothing selected > undo [Repeated 3 time(s)] > color sample #32.1 map #34 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.417, maximum 39.82 > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > show #37 models > select add #37 1 model selected > view matrix models > #37,0.70959,0.62592,0.32358,0.61324,-0.29635,0.68175,-0.66888,-0.0021786,-0.63926,0.37874,0.66925,0.69431 > close #37 > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > hide #!32 models > show #!32 models > volume #32 level 0.04587 > volume #32 level 0.04884 > key pos 0.437353,0.539212 size 0.000454748,0.0481037 > hide #36 models > show #36 models > close #36 > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > ui mousemode right translate > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true [Repeated 1 time(s)] > ui mousemode right ""color key"" > ui mousemode right translate > ui mousemode middle 'color key' > key border false > key border true > key borderWidth 1.0 > key borderWidth 0.0 > key borderWidth 1.0 > key colorTreatment distinct > key colorTreatment blended > ui mousemode middle translate > ui mousemode middle ""color key"" > key borderColor #bfbfbf > key borderColor default > key borderColor #bfbfbf > key borderColor #030303 > key borderColor #020202 > key borderColor #010202 > key borderColor black > key labelColor #bfbfbf > key labelColor default > key fontSize 23 > key fontSize 22 > key fontSize 21 > key fontSize 20 > key fontSize 21 > key fontSize 22 > key fontSize 23 > key fontSize 24 > key bold true > key italic true > key italic false > key numericLabelSpacing equal > key numericLabelSpacing proportional > key labelSide left/top > key labelSide right/bottom > key justification left > key labelSide right/bottom > key justification decimal > key justification right > key justification left > key labelOffset 1.0 > key labelOffset 2.0 > key labelOffset 3.0 > key labelOffset 4.0 > key labelOffset 5.0 > key labelOffset 4.0 > key labelOffset 3.0 > key labelOffset 2.0 > key ticks true > key ticks false > key size 0.26000,0.05000 > key size 0.27000,0.05000 > key size 0.26000,0.05000 > key size 0.25000,0.05000 > key size 0.24000,0.05000 > key size 0.23000,0.05000 > key size 0.22000,0.05000 > key size 0.22000,0.04000 > key size 0.21000,0.04000 > key size 0.20000,0.04000 > key size 0.19000,0.04000 > key bold false > key borderWidth 2.0 > key border false > key border true > key size 0.18000,0.04000 > key size 0.17000,0.04000 > key size 0.17000,0.03000 > key size 0.17000,0.02000 > key size 0.16000,0.02000 > key size 0.15000,0.02000 > key size 0.14000,0.02000 > key size 0.15000,0.02000 > key size 0.14000,0.02000 > key size 0.14000,0.01000 > key size 0.14000,0.02000 > key size 0.14000,0.01000 > key size 0.14000,0.02000 > key size 0.14000,0.03000 > key size 0.14000,0.04000 > key size 0.14000,0.03000 > key bold true > save CS_P4_J282_locres_sharp.png supersample 3 transparentBackground true > hide #!32 models > show #!33 models > show #!35 models > volume #33 level 0.0299 > undo > show #!35 models > volume #35 level 3.774 > hide #!35 models > color sample #33.1 map #35 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.383, maximum 41.2 > volume #33 level 0.03991 > volume #33 level 0.049 > volume #33 level 0.06811 > volume #33 level 0.05628 > volume #33 level 0.05719 > ui mousemode right translate [Repeated 1 time(s)] > select add #37 1 model selected > ui mousemode right translate > select subtract #37 Nothing selected > view #33 > volume #33 level 0.05264 > volume #33 level 0.05082 > save CS_P4_J285_NU_sharp.png supersample 3 transparentBackground true > save CS_P4_J285_locres_sharp.png supersample 3 transparentBackground true > hide #!33 models > show #!32 models > volume #32 level 0.05478 > save CS_P4_J282_locres_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260503_SA-F_B1_workflow1.cxs"" > show #!33 models > hide #!33 models > volume flip #32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > color sample #38.1 map #34 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.643, maximum 46.37 > select add #38 2 models selected > select subtract #38 Nothing selected > show #!34 models > hide #!34 models > show #!32 models > select add #38 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #38,0.96218,0.27239,0.0026401,-33.277,0.27218,-0.96095,-0.049909,243.62,-0.011058,0.04874,-0.99875,256.5 > fitmap #38 inMap #32 Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map cryosparc_P4_J282_005_volume_map_sharp.mrc using 208382 points correlation = 0.3998, correlation about mean = 0.04433, overlap = 423.6 steps = 132, shift = 4.37, angle = 6.4 degrees Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#38) relative to cryosparc_P4_J282_005_volume_map_sharp.mrc (#32) coordinates: Matrix rotation and translation 0.98647244 0.16384860 0.00507628 -21.42824077 0.16385811 -0.98468453 -0.05955579 259.77996198 -0.00475960 0.05958193 -0.99821207 257.16545694 Axis 0.99660933 0.08227896 0.00007951 Axis point 0.00000000 126.91521003 132.48208787 Rotation angle (degrees) 176.57330142 Shift along axis 0.03928788 > select subtract #38 Nothing selected > select add #38 2 models selected > view matrix models > #38,-0.55814,-0.81354,-0.1632,351.46,-0.79796,0.58019,-0.16319,187.27,0.22745,0.039147,-0.973,224.57 > ui mousemode right ""translate selected models"" > view matrix models > #38,-0.55814,-0.81354,-0.1632,337.55,-0.79796,0.58019,-0.16319,184.57,0.22745,0.039147,-0.973,224.6 > fitmap #38 inMap #32 Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map cryosparc_P4_J282_005_volume_map_sharp.mrc using 208382 points correlation = 0.4208, correlation about mean = 0.04628, overlap = 461.9 steps = 76, shift = 2.33, angle = 4.27 degrees Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#38) relative to cryosparc_P4_J282_005_volume_map_sharp.mrc (#32) coordinates: Matrix rotation and translation -0.49732082 -0.85447621 -0.15014131 334.86076124 -0.83743504 0.51801846 -0.17423960 201.03033487 0.22665956 0.03908062 -0.97318968 225.34606158 Axis 0.49228130 -0.86954734 0.03932608 Axis point 210.12674218 0.00000000 138.36301119 Rotation angle (degrees) 167.48677512 Shift along axis -1.09772430 > select subtract #38 Nothing selected > select add #38 2 models selected > view matrix models > #38,-0.49732,-0.85448,-0.15014,335.05,-0.83744,0.51802,-0.17424,201.05,0.22666,0.039081,-0.97319,225.03 > ui mousemode right ""rotate selected models"" > view matrix models > #38,-0.016367,0.99633,0.084023,-21.562,0.99914,0.013095,0.039355,-10.502,0.03811,0.084595,-0.99569,247.71 > ui mousemode right ""translate selected models"" > view matrix models > #38,-0.016367,0.99633,0.084023,-11.414,0.99914,0.013095,0.039355,-8.4507,0.03811,0.084595,-0.99569,248.91 > fitmap #38 inMap #32 Fit map cryosparc_P4_J282_005_volume_map_sharp.mrc z flip in map cryosparc_P4_J282_005_volume_map_sharp.mrc using 208382 points correlation = 0.4638, correlation about mean = 0.04825, overlap = 549.2 steps = 212, shift = 3.48, angle = 14 degrees Position of cryosparc_P4_J282_005_volume_map_sharp.mrc z flip (#38) relative to cryosparc_P4_J282_005_volume_map_sharp.mrc (#32) coordinates: Matrix rotation and translation -0.11733678 0.98529275 -0.12421864 36.78201449 0.98526620 0.13117004 0.10974943 -32.51895072 0.12442908 -0.10951079 -0.98616672 260.89985464 Axis -0.66139292 -0.75003960 -0.00008010 Axis point 18.21387939 0.00000000 132.49954907 Rotation angle (degrees) 170.45882216 Shift along axis 0.04223943 > select subtract #38 Nothing selected > hide #!32 models > color sample #38.1 map #34 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 3.043, mean 3.992, maximum 41.6 > show #!34 models > volume flip #34 Opened cryosparc_P4_J287_map_locres.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > select add #39 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #39,0.92903,0.36038,-0.083822,-29.473,0.36808,-0.92323,0.1103,201.34,-0.037639,-0.13332,-0.99036,275.09 > show #!34 models > fitmap #39 imapt #34 Expected a keyword > fitmap #39 inMap #34 Fit map cryosparc_P4_J287_map_locres.mrc z flip in map cryosparc_P4_J287_map_locres.mrc using 2056381 points correlation = 0.8371, correlation about mean = 0.04941, overlap = 1.057e+08 steps = 612, shift = 15.2, angle = 38.8 degrees Position of cryosparc_P4_J287_map_locres.mrc z flip (#39) relative to cryosparc_P4_J287_map_locres.mrc (#34) coordinates: Matrix rotation and translation 0.49975558 0.86379414 -0.06406286 -38.69544656 0.86380943 -0.49157793 0.11038297 66.86486459 0.06385627 -0.11050260 -0.99182234 270.06743869 Axis -0.86536171 -0.50114779 0.00005993 Axis point 0.00000000 54.63554700 132.55703766 Rotation angle (degrees) 172.66756182 Shift along axis -0.00743630 > select subtract #39 Nothing selected > hide #!39 models > show #!39 models > select add #39 2 models selected > hide #37 models > hide #!38 models > view matrix models > #39,0.37237,-0.92808,0.0029165,218.26,-0.92659,-0.37195,-0.055474,318.12,0.052569,0.017955,-0.99846,254.69 > ui mousemode right ""translate selected models"" > view matrix models > #39,0.37237,-0.92808,0.0029165,208.8,-0.92659,-0.37195,-0.055474,313.9,0.052569,0.017955,-0.99846,255.36 > ui mousemode right ""rotate selected models"" > view matrix models > #39,0.66947,-0.74091,0.05349,135.56,-0.73453,-0.67101,-0.10103,334.54,0.11074,0.028346,-0.99344,245.27 > ui mousemode right ""translate selected models"" > view matrix models > #39,0.66947,-0.74091,0.05349,211.58,-0.73453,-0.67101,-0.10103,368.3,0.11074,0.028346,-0.99344,245.76 > view matrix models > #39,0.66947,-0.74091,0.05349,241.5,-0.73453,-0.67101,-0.10103,381.69,0.11074,0.028346,-0.99344,243.08 > view matrix models > #39,0.66947,-0.74091,0.05349,287.43,-0.73453,-0.67101,-0.10103,402.31,0.11074,0.028346,-0.99344,237.25 > ui mousemode right ""rotate selected models"" > view matrix models > #39,-0.41494,0.89077,-0.18535,241.42,0.8738,0.44692,0.19168,-11.043,0.25358,-0.082424,-0.9638,229.13 > view matrix models > #39,0.99948,-0.019992,0.025148,145.79,-0.021975,-0.99645,0.081215,326.06,0.023435,-0.081726,-0.99638,264.88 > ui mousemode right ""translate selected models"" > view matrix models > #39,0.99948,-0.019992,0.025148,-4.0949,-0.021975,-0.99645,0.081215,259.26,0.023435,-0.081726,-0.99638,270.42 > select subtract #39 Nothing selected > hide #!34 models > color sample #38.1 map #34 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 3.043, mean 3.992, maximum 41.6 > hide #!39 models > show #!38 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J282_005_volume_map_sharp.mrc"" Opened cryosparc_P4_J282_005_volume_map_sharp.mrc as #40, grid size 320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32 > hide #!38 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J287_map_locres.mrc"" Opened cryosparc_P4_J287_map_locres.mrc as #41, grid size 320,320,320, pixel 0.831, shown at level 9.77, step 2, values float32 > volume flip #40 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #42, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #41 Opened cryosparc_P4_J287_map_locres.mrc z flip as #43, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume #43 level 4.042 > color sample #42.1 map #43 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.484, maximum 42.57 > hide #!43 models > hide #!42 models > show #!38 models > show #!39 models > show #!40 models > show #!41 models > show #!42 models > show #!43 models > close #43 > close #38 > close #42 > close #41 > close #40 > close #39 > close #37 > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > hide #36 models > volume flip #32 Opened cryosparc_P4_J282_005_volume_map_sharp.mrc z flip as #37, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #34 Opened cryosparc_P4_J287_map_locres.mrc z flip as #38, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #33 Opened cryosparc_P4_J285_006_volume_map_sharp.mrc z flip as #39, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #35 Opened cryosparc_P4_J288_map_locres.mrc z flip as #40, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > hide #!39 models > hide #!40 models > hide #!38 models > color sample #37.1 map #38 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.731, maximum 41.43 > hide #!37 models > show #!37 models > hide #!37 models > show #!39 models > color sample #39.1 map #40 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.67, maximum 40.73 > volume #39 level 0.05082 > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > show #36 models > select add #36 1 model selected > key pos 0.366468,0.16715 > key pos 0.360149,0.168599 > key labelColor #bfbfbf > key labelColor default > key labelColor #bfbfbf > key labelColor white > key labelColor default > key ticks true > key tickLength 8.0 > key tickThickness 3.0 > key tickThickness 2.0 > key tickThickness 1.0 > key tickLength 10.0 > key tickLength 8.0 > key tickThickness 2.0 > key tickThickness 1.0 > key tickThickness 0.0 > key tickThickness 1.0 > key tickThickness 2.0 > key ticks false > key labelOffset -1.0 > key labelOffset -2.0 > key labelOffset -1.0 > key labelOffset 0.0 > key labelOffset 1.0 > key labelOffset 2.0 > key labelOffset 3.0 > key labelOffset 4.0 > view matrix models #36,1,0,0,-0.86321,0,1,0,-0.41592,0,0,1,0.9887 > select subtract #36 Nothing selected > select add #36 1 model selected > view matrix models #36,1,0,0,-99.598,0,1,0,-41.849,0,0,1,63.569 > view matrix models #36,1,0,0,-99.715,0,1,0,-41.895,0,0,1,63.621 > view matrix models #36,1,0,0,-102.61,0,1,0,-42.915,0,0,1,63.831 > view matrix models #36,1,0,0,-126.49,0,1,0,-56.195,0,0,1,105.79 > view matrix models #36,1,0,0,-152.42,0,1,0,-56.013,0,0,1,31.21 > view matrix models #36,1,0,0,-131.29,0,1,0,-47.985,0,0,1,24.738 > view matrix models #36,1,0,0,-121.36,0,1,0,-44.649,0,0,1,25.261 > view matrix models #36,1,0,0,-121.37,0,1,0,-44.69,0,0,1,25.567 > view matrix models #36,1,0,0,-123.18,0,1,0,-45.336,0,0,1,25.776 > close #36 > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > key pos 0.377773,0.195303 > key pos 0.377554,0.185959 > key borderWidth 3.0 > key labelOffset 1.0 > key labelOffset 2.0 > key labelOffset 3.0 > key labelOffset 4.0 > key labelOffset 5.0 > key labelOffset 6.0 > key size 0.24000,0.05000 > key size 0.23000,0.05000 > key size 0.23000,0.04000 > key size 0.23000,0.03000 > key size 0.22000,0.03000 > key size 0.21000,0.03000 > key size 0.20000,0.03000 > key size 0.19000,0.03000 > key size 0.18000,0.03000 > key size 0.17000,0.03000 > key size 0.16000,0.03000 > key size 0.15000,0.03000 > key size 0.16000,0.03000 > key size 0.17000,0.03000 > key size 0.17000,0.04000 > key size 0.17000,0.05000 > key size 0.17000,0.04000 > key pos 0.36134,0.205524 size 0.0323267,0.199875 > key pos 0.375585,0.243532 size 0.000780577,0.00120384 > key pos 0.393081,0.282969 size 0,0 [Repeated 1 time(s)] > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > hide #!39 models > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > key pos 0.654167,0.35194 size 0.0389145,0.208023 > show #!39 models > key pos 0.434243,0.168612 size 0.0379186,0.161115 > hide #41 models > ui mousemode right ""translate selected models"" > ui mousemode right translate [Repeated 1 time(s)] > select add #41 1 model selected > select subtract #41 Nothing selected > show #41 models > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right select > select clear > ui mousemode right rotate > ui mousemode right translate > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true [Repeated 1 time(s)] > ui mousemode right zoom > ui mousemode right ""translate selected models"" > ui mousemode right select > select clear > select add #41 1 model selected > select clear Drag select of 39 cryosparc_P4_J285_006_volume_map_sharp.mrc z flip > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > select clear Drag select of 39 cryosparc_P4_J285_006_volume_map_sharp.mrc z flip > ui mousemode right translate > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > select subtract #41 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right rotate > ui mousemode right translate > hide #!39 models > show #!39 models > ui mousemode right select > select #39 2 models selected > ui mousemode right rotate > ui mousemode right translate > select subtract #39 Nothing selected > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > hide #!39 models > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode left ""color key"" > ui mousemode left rotate > ui mousemode right 'color key' > key pos 0.683937,0.290603 size 0.0366198,0.178803 > show #!39 models > key pos 0.885363,0.663755 size 0.0185522,0.00687018 > ui mousemode right translate > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > key pos 0.768821,0.24433 size 0.0347996,0.266198 > key labelOffset 7.0 > key labelOffset 8.0 > key labelOffset 9.0 > hide #!39 models > show #!37 models > volume #37 level 0.06504 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260503_SA-F_B1_workflow2.cxs"" > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > key fontSize 25 > key fontSize 26 > key fontSize 27 > key fontSize 28 > key fontSize 29 > key fontSize 30 > key fontSize 31 > key fontSize 32 > key fontSize 33 > key fontSize 34 > key fontSize 35 > save CS_P4_J282_locres_sharp.png supersample 3 transparentBackground true > hide #!37 models > show #!39 models > volume #39 level 0.06897 > volume #39 level 0.06638 > save CS_P4_J285_locres_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260503_SA-F_B1_workflow2.cxs"" > hide #!39 models > hide #41 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/CS_P4_J282_sharp_flip.mrc"" Opened CS_P4_J282_sharp_flip.mrc as #42, grid size 320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe University/19. Model Building/2. AcrF > Project/2. Bound-form/SA-F_B1/Model/aligned_model_for_J282.pdb"" Chain information for aligned_model_for_J282.pdb #43 --- Chain | Description A B C | No description available > hide #!42 models > select #43/BC Nothing selected > select #43/B, C 15672 atoms, 15966 bonds, 2068 residues, 1 model selected > delete sel > show #!42 models > volume zone #42 nearAtoms #43/A > color #43 #FFF6C0 > volume zone #42 nearAtoms #43/A distance 5 Expected a keyword > color zone #42 near #43/A distance 5 > color zone #42 near #43/A distance 5 tran 50 Expected a keyword > color zone #42 near #43/A distance 5 tran 50 Expected a keyword > color #43 #FFF6C0 > color zone #42 near #43/A distance 5 > color #43 #FFF6C0 transparency 50 > color zone #42 near #43/A distance 5 > graphics silhouettes false > lighting full > lighting flat [Repeated 1 time(s)] > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft [Repeated 1 time(s)] > lighting simple > graphics silhouettes false > color #42 #99bfe580 models > hide #43 models > transparency #42 50 > lighting soft > volume #42 level 0.0232 > lighting soft > close #42 > close #43 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J242_class_02_00122_volume_sharp.mrc"" Opened cryosparc_P4_J242_class_02_00122_volume_sharp.mrc as #36, grid size 128,128,128, pixel 2.08, shown at level 0.195, step 1, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J242_class_01_00122_volume_sharp.mrc"" Opened cryosparc_P4_J242_class_01_00122_volume_sharp.mrc as #42, grid size 128,128,128, pixel 2.08, shown at level 0.178, step 1, values float32 > close #36 > show #!9 models > select add #42 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #42,0.026241,-0.92593,0.37678,198.52,-0.063177,0.37462,0.92502,-34.721,-0.99766,-0.048078,-0.048667,279.22 > ui mousemode right ""translate selected models"" > view matrix models > #42,0.026241,-0.92593,0.37678,198.7,-0.063177,0.37462,0.92502,-33.267,-0.99766,-0.048078,-0.048667,263 > fitmap #42 inMap #9 Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc using 20960 points correlation = 1, correlation about mean = 1, overlap = 1571 steps = 128, shift = 5.08, angle = 27.9 degrees Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#42) relative to cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.99999999 -0.00010909 0.00000609 0.02020954 0.00010909 0.99999995 0.00031305 -0.06272325 -0.00000612 -0.00031305 0.99999995 0.03217050 Axis -0.94414385 0.01842055 0.32901836 Axis point 0.00000000 112.87704178 199.81299213 Rotation angle (degrees) 0.01899762 Shift along axis -0.00965143 > select subtract #42 Nothing selected > select add #42 2 models selected > fitmap #42 inMap #9 Fit map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc in map cryosparc_P4_J242_class_01_00122_volume_sharp.mrc using 20960 points correlation = 1, correlation about mean = 1, overlap = 1571 steps = 40, shift = 0.00318, angle = 0.00769 degrees Position of cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#42) relative to cryosparc_P4_J242_class_01_00122_volume_sharp.mrc (#9) coordinates: Matrix rotation and translation 0.99999999 -0.00011772 0.00012933 0.00283694 0.00011769 0.99999996 0.00026066 -0.05912201 -0.00012937 -0.00026064 0.99999996 0.04294746 Axis -0.83040251 0.41209275 0.37498166 Axis point 0.00000000 180.01203882 210.06369623 Rotation angle (degrees) 0.01798432 Shift along axis -0.01061505 > select subtract #42 Nothing selected > hide #!9 models > volume #42 level 0.2579 > color #42 #ffffb2ff models > color #42 #ffffb280 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/CS_P4_J282_sharp_flip.mrc"" Opened CS_P4_J282_sharp_flip.mrc as #36, grid size 320,320,320, pixel 0.831, shown at level 0.0392, step 2, values float32 > volume #42 level 0.1954 > select add #42 2 models selected > view matrix models > #42,0.15189,-0.98482,-0.084022,248.42,-0.056394,-0.093504,0.99402,24.018,-0.98679,-0.14625,-0.069741,273.86 > volume #42 level 0.2537 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J169_class_03_00182_volume_sharp.mrc"" Opened cryosparc_P4_J169_class_03_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.248, step 1, values float32 > close #43 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J169_class_02_00182_volume_sharp.mrc"" Opened cryosparc_P4_J169_class_02_00182_volume_sharp.mrc as #43, grid size 128,128,128, pixel 2.08, shown at level 0.216, step 1, values float32 > select add #43 4 models selected > view matrix models > #42,0.15189,-0.98482,-0.084022,246.73,-0.056394,-0.093504,0.99402,-45.124,-0.98679,-0.14625,-0.069741,235.92,#43,1,0,0,-1.6882,0,1,0,-69.141,0,0,1,-37.947 > view matrix models > #42,0.15189,-0.98482,-0.084022,237,-0.056394,-0.093504,0.99402,126.12,-0.98679,-0.14625,-0.069741,312.08,#43,1,0,0,-11.419,0,1,0,102.11,0,0,1,38.221 > select subtract #42 2 models selected > view matrix models #43,1,0,0,-10.922,0,1,0,105.75,0,0,1,25.23 > ui mousemode right ""rotate selected models"" > view matrix models > #43,0.053361,-0.96815,-0.24461,270.41,-0.10024,-0.24891,0.96332,141.36,-0.99353,-0.026885,-0.11033,315.47 > ui mousemode right ""translate selected models"" > view matrix models > #43,0.053361,-0.96815,-0.24461,276.43,-0.10024,-0.24891,0.96332,50.344,-0.99353,-0.026885,-0.11033,257.37 > ui mousemode right ""rotate selected models"" > view matrix models > #43,0.25016,-0.91768,-0.30868,252.37,-0.0074281,-0.32063,0.94718,48.872,-0.96818,-0.23465,-0.087026,276.42 > ui mousemode right ""translate selected models"" > view matrix models > #43,0.25016,-0.91768,-0.30868,252.17,-0.0074281,-0.32063,0.94718,49.119,-0.96818,-0.23465,-0.087026,280.28 > view matrix models > #43,0.25016,-0.91768,-0.30868,245.18,-0.0074281,-0.32063,0.94718,41.479,-0.96818,-0.23465,-0.087026,278.46 > view matrix models > #43,0.25016,-0.91768,-0.30868,244.24,-0.0074281,-0.32063,0.94718,46.881,-0.96818,-0.23465,-0.087026,278.05 > select add #42 4 models selected > select subtract #43 2 models selected > view matrix models > #42,0.15189,-0.98482,-0.084022,248.26,-0.056394,-0.093504,0.99402,10.768,-0.98679,-0.14625,-0.069741,272.27 > select subtract #42 Nothing selected > color #36 #99BFE5 > hide #!42 models > select add #43 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #43,0.073784,-0.55439,0.82898,66.918,0.0052521,0.83145,0.55558,-43.45,-0.99726,-0.036639,0.064259,236.72 > ui mousemode right ""translate selected models"" > view matrix models > #43,0.073784,-0.55439,0.82898,82.905,0.0052521,0.83145,0.55558,-39.115,-0.99726,-0.036639,0.064259,236.78 > select subtract #43 Nothing selected > volume #36 level 0.0602 > select add #43 2 models selected > view matrix models > #43,0.073784,-0.55439,0.82898,84.941,0.0052521,0.83145,0.55558,-38.546,-0.99726,-0.036639,0.064259,236.53 > view matrix models > #43,0.073784,-0.55439,0.82898,84.833,0.0052521,0.83145,0.55558,-38.074,-0.99726,-0.036639,0.064259,236.34 > volume #43 level 0.1902 > color #43 #b2b2ff80 models > volume #43 level 0.2283 > select add #40 4 models selected > select subtract #40 2 models selected > select subtract #43 Nothing selected > color #43 #ffffb280 models > color #43 #b2b2ff80 models > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260503_SA-F_B1_workflow3.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_cryosparc_P4_J243_003_volume_map_35_TMD_regions_resampled.mrc"" Opened cryosparc_P4_cryosparc_P4_J243_003_volume_map_35_TMD_regions_resampled.mrc as #44, grid size 80,80,80, pixel 3.32, shown at level 0.324, step 1, values float32 > close #44 > save CS_P4_J282_show_mask_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260503_SA-F_B1_workflow4.cxs"" ——— End of log from Sun May 3 17:29:06 2026 ——— > view name session-start opened ChimeraX session > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J295_006_volume_map_sharp.mrc"" Opened cryosparc_P4_J295_006_volume_map_sharp.mrc as #44, grid size 320,320,320, pixel 0.831, shown at level 0.0361, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J296_map_locres.mrc"" Opened cryosparc_P4_J296_map_locres.mrc as #45, grid size 320,320,320, pixel 0.831, shown at level 8.66, step 2, values float32 > hide #!43 models > hide #!36 models > hide #!45 models > show #!45 models > hide #!45 models > volume flip #44 Opened cryosparc_P4_J295_006_volume_map_sharp.mrc z flip as #46, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #45 Opened cryosparc_P4_J296_map_locres.mrc z flip as #47, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #45 > close #44 > rename #46 CS_P4_J295_sharp_flip id #44 > save CS_P4_J295_sharp_flip.mrc #44 > rename #47 CS_P4_J296_locres_flip id #45 > save CS_P4_J296_locres_flip.mrc #45 > ui tool show ""Surface Color"" > hide #!45 models > color sample #44.1 map #45 palette #ffb17f:#527dea:#99bfe5:#fff6c0:#f4fff3 > outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.132, maximum 48.35 > show #41 models > volume #44 level 0.0515 > color sample #44.1 map #45 palette > 1,#ffb17f:2,#527dea:3,#99bfe5:4,#fff6c0:5,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#ffb17f:3,#527dea:4,#ffb17f:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#527dea:3,#99bfe5:4,#ffb17f:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > key #527dea:2 #99bfe5:3 #ffb17f:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#527dea outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > key #f4fff3:2 #fff6c0:3 #ffb17f:4 #99bfe5:5 #527dea:6 showTool true > ui mousemode right ""color key"" > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#527dd6 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#46a2de outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#4d8fde outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#94aec1 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#a78bc1 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#c1a77f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#f4fff3:3,#fff6c0:4,#ffb17f:5,#99bfe5:6,#89b3c1 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#ffb17f:3,#527dea:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > key #ffb17f:2 #527dea:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > color sample #44.1 map #45 palette > 2,#ffb17f:3,#2c98ee:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > color sample #44.1 map #45 palette > 2,#ffb17f:3,#4979d3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 3.583, maximum 39.22 > save CS_P4_J295_locres_sharp.png supersample 3 transparentBackground true Cell requested for row 0 is out of bounds for table with 6 rows! Resizing table model. > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260505_SA-F_B1_workflow.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J300_005_volume_map_sharp.mrc"" Opened cryosparc_P4_J300_005_volume_map_sharp.mrc as #46, grid size 320,320,320, pixel 0.831, shown at level 0.0375, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J301_map_locres.mrc"" Opened cryosparc_P4_J301_map_locres.mrc as #47, grid size 320,320,320, pixel 0.831, shown at level 9.68, step 2, values float32 > hide #!44 models > hide #!47 models > volume flip #46 Opened cryosparc_P4_J300_005_volume_map_sharp.mrc z flip as #48, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #47 Opened cryosparc_P4_J301_map_locres.mrc z flip as #49, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #46 > close #47 > rename #48 CS_P4_J300_sharp_flip id #46 > rename #49 CS_P4_J301_locres_flip id #47 > save CS_P4_J301_locres_flip.mrc #47 > save CS_P4_J300_sharp_flip.mrc #46 > color sample #46.1 map #47 palette > 2,#ffb17f:3,#4979d3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.498, maximum 44.88 > hide #!47 models > volume #46 level 0.03399 > volume #46 level 0.06962 > volume #46 level 0.05919 > save CS_P4_J300_locres_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260505_SA-F_B1_workflow.cxs"" ——— End of log from Tue May 5 09:31:57 2026 ——— > view name session-start opened ChimeraX session > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J302_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J302_002_volume_map_sharp.mrc as #48, grid size 80,80,80, pixel 3.32, shown at level 0.658, step 1, values float32 > select add #48 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #48,0.064602,0.97911,0.19278,-26.266,0.98732,-0.034646,-0.1549,22.036,-0.14498,0.20034,-0.96894,229.94 > volume flip #48 Opened cryosparc_P4_J302_002_volume_map_sharp.mrc z flip as #49, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #48 > rename #49 rename > rename #49 CS_P4_J302_sharp_flip id #48 > save CS_P4_J302_sharp_flip.mrc #48 > select add #48 2 models selected > view matrix models > #48,-0.56486,-0.82475,0.026783,324.58,0.77395,-0.54076,-0.32951,143.72,0.28625,-0.1654,0.94377,-52.222 > hide #41 models > hide #!46 models > show #!47 models > hide #!47 models > show #!45 models > hide #!45 models > show #!43 models > hide #!43 models > show #!39 models > ui mousemode right ""translate selected models"" > view matrix models > #48,-0.56486,-0.82475,0.026783,319.51,0.77395,-0.54076,-0.32951,139.04,0.28625,-0.1654,0.94377,-3.8614 > view matrix models > #48,-0.56486,-0.82475,0.026783,321.32,0.77395,-0.54076,-0.32951,140.03,0.28625,-0.1654,0.94377,-10.821 > fitmap $48 inmap #39 Missing or invalid ""atomsOrMap"" argument: invalid objects specifier > fitmap #48 inMap #39 Fit map CS_P4_J302_sharp_flip.mrc in map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip using 5112 points correlation = 0.3608, correlation about mean = 0.02111, overlap = 103.8 steps = 76, shift = 4.71, angle = 3.71 degrees Position of CS_P4_J302_sharp_flip.mrc (#48) relative to cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#39) coordinates: Matrix rotation and translation -0.54436883 -0.83749052 0.04766738 317.13056079 0.79848148 -0.53475206 -0.27652762 129.04232256 0.25707950 -0.11247150 0.95982304 -11.58663120 Axis 0.09898047 -0.12634523 0.98703584 Axis point 124.28808276 149.04371086 0.00000000 Rotation angle (degrees) 124.03152255 Shift along axis 3.64942894 > ui mousemode right ""rotate selected models"" > view matrix models > #48,-0.38435,0.91427,-0.12797,86.018,-0.92117,-0.38898,-0.012326,307,-0.061046,0.11314,0.9917,-2.8083 > fitmap #48 inMap #39 Fit map CS_P4_J302_sharp_flip.mrc in map cryosparc_P4_J285_006_volume_map_sharp.mrc z flip using 5112 points correlation = 0.623, correlation about mean = 0.1973, overlap = 254 steps = 104, shift = 5.55, angle = 8.62 degrees Position of CS_P4_J302_sharp_flip.mrc (#48) relative to cryosparc_P4_J285_006_volume_map_sharp.mrc z flip (#39) coordinates: Matrix rotation and translation -0.49090927 0.85957769 -0.14189522 105.36638005 -0.85910240 -0.50468247 -0.08508012 328.20339808 -0.14474501 0.08013591 0.98621858 12.70754555 Axis 0.09568836 0.00165051 -0.99540997 Axis point 147.88121154 133.69042072 0.00000000 Rotation angle (degrees) 120.31054935 Shift along axis -2.02517664 > select subtract #48 Nothing selected > volume #48 level 0.8066 > hide #!48 models > show #!48 models > hide #!39 models > show #!40 models > hide #!40 models > show #!46 models > hide #!46 models > show #!46 models > hide #!46 models > volume #48 level 0.6121 > show #!24 models > hide #!24 models > color #48 #99BFE5 > hide #!48 models > show #!48 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J303_003_volume_map_sharp.mrc"" Opened cryosparc_P4_J303_003_volume_map_sharp.mrc as #49, grid size 80,80,80, pixel 3.32, shown at level 0.57, step 1, values float32 > select add #49 2 models selected > view matrix models > #49,0.53874,0.84077,0.053573,-61.438,0.83514,-0.54134,0.097405,87.116,0.1109,-0.0077344,-0.9938,260.56 > view matrix models > #49,0.53215,0.84494,0.053856,-61.154,0.83957,-0.53484,0.095262,85.896,0.10929,-0.0054773,-0.99399,260.49 > view matrix models > #49,-0.8763,-0.44891,0.17485,296.18,-0.45964,0.88777,-0.024369,82.131,-0.14428,-0.10172,-0.98429,307.41 > volume flip #49 Opened cryosparc_P4_J303_003_volume_map_sharp.mrc z flip as #50, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #49 > rename #50 CS_P4_J303_sharp_flip id #49 > save CS_P4_J303_sharp_flip.mrc #49 > select add #49 2 models selected > view matrix models > #49,-0.44927,0.88595,-0.11509,87.376,-0.86051,-0.46376,-0.21085,349.13,-0.24018,0.0043123,0.97072,61.749 > ui mousemode right ""translate selected models"" > view matrix models > #49,-0.44927,0.88595,-0.11509,93.572,-0.86051,-0.46376,-0.21085,352.06,-0.24018,0.0043123,0.97072,37.843 > fitmap #49 inMap 348 Invalid ""inMap"" argument: invalid density map specifier > fitmap #49 inMap #48 Fit map CS_P4_J303_sharp_flip.mrc in map CS_P4_J302_sharp_flip.mrc using 5118 points correlation = 0.8483, correlation about mean = 0.4386, overlap = 3011 steps = 68, shift = 10.7, angle = 7.19 degrees Position of CS_P4_J303_sharp_flip.mrc (#49) relative to CS_P4_J302_sharp_flip.mrc (#48) coordinates: Matrix rotation and translation 0.99996126 -0.00401528 0.00783497 -1.22617333 0.00399514 0.99998870 0.00258400 -1.26181412 -0.00784526 -0.00255260 0.99996598 1.34185977 Axis -0.28004899 0.85489100 0.43673098 Axis point 178.64594040 0.00000000 162.72002408 Rotation angle (degrees) 0.52546068 Shift along axis -0.14929320 > select subtract #49 Nothing selected > hide #!48 models > color #49 #FCEDFF > hide #!49 models > show #!49 models > volume #49 level 0.5753 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J304_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J304_002_volume_map_sharp.mrc as #50, grid size 80,80,80, pixel 3.32, shown at level 1.66, step 1, values float32 > hide #!49 models > select add #50 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #50,0.25626,0.96633,0.023099,-33.544,0.9662,-0.25539,-0.035012,44.222,-0.027934,0.03129,-0.99912,256.23 > volume #50 level 2.579 > select subtract #50 Nothing selected > volume #50 level 1.975 > volume flip #50 Opened cryosparc_P4_J304_002_volume_map_sharp.mrc z flip as #51, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #50 > rename #51 CS_P4_J304_sharp_flip id #50 > save CS_P4_J304_sharp_flip.mrc #50 > select add #50 2 models selected > show #!49 models > view matrix models > #50,0.25432,0.96619,0.042346,-35.759,0.96711,-0.25431,-0.0057645,40.158,0.0051995,0.042419,-0.99909,250.22 > view matrix models > #50,-0.77557,0.61543,-0.14049,175.22,-0.61485,-0.78688,-0.052719,333.03,-0.143,0.045495,0.98868,11.993 > color #50 #FCEDFF > select subtract #50 Nothing selected > hide #!49 models > hide #!50 models > show #!50 models > volume #50 level 1.954 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J305_003_volume_map_sharp.mrc"" Opened cryosparc_P4_J305_003_volume_map_sharp.mrc as #51, grid size 80,80,80, pixel 3.32, shown at level 0.569, step 1, values float32 > hide #!50 models > select add #51 2 models selected > view matrix models > #51,-0.9391,-0.22026,0.26379,268.58,-0.1463,0.9508,0.27307,-8.1662,-0.31096,0.21785,-0.92512,264.01 > volume flip #51 Opened cryosparc_P4_J305_003_volume_map_sharp.mrc z flip as #52, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #51 > rename #52 CS_P4_J305_sharp_flip id #51 > save CS_P4_J305_sharp_flip.mrc #51 > color #51 #FCEDFF > show #!50 models > select add #51 2 models selected > view matrix models > #51,0.99548,-0.078687,0.053201,5.068,0.073705,0.99322,0.089881,-20.578,-0.059913,-0.085553,0.99453,15.159 > fitmap #51 inMap #50 Fit map CS_P4_J305_sharp_flip.mrc in map CS_P4_J304_sharp_flip.mrc using 5112 points correlation = 0.7769, correlation about mean = 0.3462, overlap = 4325 steps = 92, shift = 6.39, angle = 27.1 degrees Position of CS_P4_J305_sharp_flip.mrc (#51) relative to CS_P4_J304_sharp_flip.mrc (#50) coordinates: Matrix rotation and translation -0.48191930 -0.86211205 -0.15657780 337.25915719 0.86174903 -0.49867166 0.09335524 70.84333299 -0.15856359 -0.08994107 0.98324371 36.25215794 Axis -0.10573285 0.00114549 0.99439391 Axis point 149.95468753 133.49561797 0.00000000 Rotation angle (degrees) 119.91228641 Shift along axis 0.47070508 > select subtract #51 Nothing selected > hide #!50 models > hide #!51 models > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J306_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J306_002_volume_map_sharp.mrc as #52, grid size 80,80,80, pixel 3.32, shown at level 0.89, step 1, values float32 > select add #52 2 models selected > view matrix models > #52,0.64736,0.71151,-0.27328,-15.881,0.69766,-0.69754,-0.16345,155.65,-0.30692,-0.084848,-0.94795,287.9 > volume flip #52 Opened cryosparc_P4_J306_002_volume_map_sharp.mrc z flip as #53, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #52 > select add #53 2 models selected > show #!51 models > view matrix models > #53,-0.54969,0.82414,-0.13652,114.28,-0.83504,-0.54665,0.062273,314.18,-0.023306,0.14823,0.98868,-59.023 > ui mousemode right ""translate selected models"" > view matrix models > #53,-0.54969,0.82414,-0.13652,112.71,-0.83504,-0.54665,0.062273,313.11,-0.023306,0.14823,0.98868,-22.329 > fitmap #53 inMap #51 Fit map cryosparc_P4_J306_002_volume_map_sharp.mrc z flip in map CS_P4_J305_sharp_flip.mrc using 5118 points correlation = 0.8696, correlation about mean = 0.2872, overlap = 4918 steps = 72, shift = 6.47, angle = 20.6 degrees Position of cryosparc_P4_J306_002_volume_map_sharp.mrc z flip (#53) relative to CS_P4_J305_sharp_flip.mrc (#51) coordinates: Matrix rotation and translation -0.48951817 0.85648171 -0.16374082 109.67271887 -0.85572951 -0.50794021 -0.09860917 331.28158536 -0.16762749 0.09184687 0.98156263 12.77250071 Axis 0.11055185 0.00225605 -0.99386780 Axis point 150.74970822 134.14339059 0.00000000 Rotation angle (degrees) 120.52723515 Shift along axis 0.17773418 > select subtract #53 Nothing selected > hide #!51 models > rename #53 CS_P4_J306_sharp_flip id #52 > save CS_P4_J306_sharp_flip.mrc #52 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J307_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J307_002_volume_map_sharp.mrc as #53, grid size 80,80,80, pixel 3.32, shown at level 0.417, step 1, values float32 > hide #!52 models > select add #53 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #53,-0.97802,-0.15767,0.13647,275.15,-0.15325,0.98728,0.042392,17.478,-0.14141,0.020547,-0.98974,260.92 > volume flip #53 Opened cryosparc_P4_J307_002_volume_map_sharp.mrc z flip as #54, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #53 > select add #54 2 models selected > show #!51 models > view matrix models > #54,-0.83454,0.54308,0.09272,165.84,-0.53719,-0.83947,0.081916,314.21,0.12232,0.018554,0.99232,-51.868 > ui mousemode right ""translate selected models"" > view matrix models > #54,-0.83454,0.54308,0.09272,166.01,-0.53719,-0.83947,0.081916,312.6,0.12232,0.018554,0.99232,-21.112 > fitmap #54 inMap #51 Fit map cryosparc_P4_J307_002_volume_map_sharp.mrc z flip in map CS_P4_J305_sharp_flip.mrc using 5118 points correlation = 0.9157, correlation about mean = 0.3086, overlap = 1346 steps = 92, shift = 8.03, angle = 16.7 degrees Position of cryosparc_P4_J307_002_volume_map_sharp.mrc z flip (#54) relative to CS_P4_J305_sharp_flip.mrc (#51) coordinates: Matrix rotation and translation -0.49196091 0.85478647 -0.16527113 110.59805296 -0.85414546 -0.51062861 -0.09845785 330.98838770 -0.16855261 0.09272817 0.98132130 13.11747971 Axis 0.11118076 0.00190829 -0.99379837 Axis point 150.81392912 133.83273648 0.00000000 Rotation angle (degrees) 120.70607669 Shift along axis -0.10813355 > select subtract #54 Nothing selected > rename #54 CS_P4_J307_sharp_flip id #53 > save CS_P4_J307_sharp_flip.mrc #53 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J308_003_volume_map_sharp.mrc"" Opened cryosparc_P4_J308_003_volume_map_sharp.mrc as #54, grid size 80,80,80, pixel 3.32, shown at level 0.487, step 1, values float32 > hide #!51 models > hide #!53 models > select add #54 2 models selected > view matrix models #54,1,0,0,-2.2085,0,1,0,5.106,0,0,1,17.329 > ui mousemode right ""rotate selected models"" > view matrix models > #54,-0.97907,-0.098429,0.17813,263.99,-0.078474,0.99017,0.11581,3.2524,-0.18778,0.099408,-0.97717,270.12 > volume flip #54 Opened cryosparc_P4_J308_003_volume_map_sharp.mrc z flip as #55, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #54 > select add #55 2 models selected > show #!53 models > view matrix models > #55,-0.032009,-0.99944,0.0094019,279.03,0.99475,-0.030941,0.097574,-4.0943,-0.097229,0.012476,0.99518,-8.8511 > ui mousemode right ""translate selected models"" > view matrix models > #55,-0.032009,-0.99944,0.0094019,275.5,0.99475,-0.030941,0.097574,4.3503,-0.097229,0.012476,0.99518,10.879 > fitmap #55 inMap #53 Fit map cryosparc_P4_J308_003_volume_map_sharp.mrc z flip in map CS_P4_J307_sharp_flip.mrc using 5116 points correlation = 0.9635, correlation about mean = 0.3444, overlap = 1309 steps = 80, shift = 11, angle = 8.02 degrees Position of cryosparc_P4_J308_003_volume_map_sharp.mrc z flip (#55) relative to CS_P4_J307_sharp_flip.mrc (#53) coordinates: Matrix rotation and translation -0.47079667 0.87008681 -0.14594324 102.09450866 -0.87101131 -0.48471046 -0.07996914 326.37268834 -0.14032031 0.08946901 0.98605553 9.07494900 Axis 0.09685875 -0.00321433 -0.99529295 Axis point 148.07793015 132.95152312 0.00000000 Rotation angle (degrees) 118.99450917 Shift along axis -0.19255539 > select subtract #55 Nothing selected > hide #!53 models > color #55 #fcedffff models > rename #55 CS_P4_J308_sharp_flip id #54 > save CS_P4_J308_sharp_flip.mrc #54 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J309_002_volume_map_sharp.mrc"" Opened cryosparc_P4_J309_002_volume_map_sharp.mrc as #55, grid size 80,80,80, pixel 3.32, shown at level 0.427, step 1, values float32 > hide #!54 models > select add #55 2 models selected > show #!54 models > ui mousemode right ""rotate selected models"" > view matrix models > #55,0.72482,-0.68817,-0.032661,133.9,-0.68882,-0.72298,-0.053201,331.74,0.012998,0.061058,-0.99805,234.36 > hide #!54 models > view matrix models > #55,-0.98503,0.14104,0.099091,242.98,0.14443,0.98912,0.027904,-21.89,-0.094078,0.041798,-0.99469,251.29 > volume flip #55 Opened cryosparc_P4_J309_002_volume_map_sharp.mrc z flip as #56, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #55 > select add #56 2 models selected > show #!54 models > view matrix models > #56,-0.63923,0.76709,0.054278,117.91,-0.76391,-0.64153,0.069883,315.42,0.088428,0.0032076,0.99608,-48.086 > ui mousemode right ""translate selected models"" > view matrix models > #56,-0.63923,0.76709,0.054278,118.17,-0.76391,-0.64153,0.069883,313.6,0.088428,0.0032076,0.99608,-18.356 > fitmap #56 inMap #54 Fit map cryosparc_P4_J309_002_volume_map_sharp.mrc z flip in map CS_P4_J308_sharp_flip.mrc using 5111 points correlation = 0.9585, correlation about mean = 0.3571, overlap = 1283 steps = 104, shift = 10.8, angle = 17.1 degrees Position of cryosparc_P4_J309_002_volume_map_sharp.mrc z flip (#56) relative to CS_P4_J308_sharp_flip.mrc (#54) coordinates: Matrix rotation and translation -0.48831434 -0.86312376 -0.12871093 333.56502617 0.86459679 -0.49852007 0.06285020 75.43057430 -0.11841248 -0.08059241 0.98968852 28.18171624 Axis -0.08273806 -0.00594017 0.99655362 Axis point 146.06051902 134.60897835 0.00000000 Rotation angle (degrees) 119.90563147 Shift along axis 0.03799683 > select subtract #56 Nothing selected > hide #!54 models > hide #!56 models > show #!56 models > color #56 #fcedffff models > rename #56 CS_P4_J309_sharp_flip id #55 > save CS_P4_J309_sharp_flip.mrc #55 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J310_003_volume_map_sharp.mrc"" Opened cryosparc_P4_J310_003_volume_map_sharp.mrc as #56, grid size 80,80,80, pixel 3.32, shown at level 0.683, step 1, values float32 > volume flip #56 Opened cryosparc_P4_J310_003_volume_map_sharp.mrc z flip as #57, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #56 > fitmap #56 inMap #52 No atoms or maps for #56 > fitmap #57 inMap #52 Fit map cryosparc_P4_J310_003_volume_map_sharp.mrc z flip in map CS_P4_J306_sharp_flip.mrc using 5115 points correlation = 0.769, correlation about mean = 0.3701, overlap = 4288 steps = 88, shift = 5.42, angle = 22.7 degrees Position of cryosparc_P4_J310_003_volume_map_sharp.mrc z flip (#57) relative to CS_P4_J306_sharp_flip.mrc (#52) coordinates: Matrix rotation and translation -0.48166864 -0.85899522 -0.17355843 339.66736714 0.86194402 -0.50013127 0.08319372 72.72621082 -0.15826501 -0.10952585 0.98130335 38.95738038 Axis -0.11128512 -0.00883113 0.99374928 Axis point 150.89500052 135.18260516 0.00000000 Rotation angle (degrees) 120.01642768 Shift along axis 0.27169032 > hide #!55 models > show #!52 models > color #57 #fcedffff models > hide #!52 models > save #57 CS_P4_J310_sharp_flip id #56 Cannot determine format for '#57' > rename #57 CS_P4_J310_sharp_flip id #56 > save CS_P4_J310_sharp_flip.mrc #56 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J311_004_volume_map_sharp.mrc"" Opened cryosparc_P4_J311_004_volume_map_sharp.mrc as #57, grid size 80,80,80, pixel 3.32, shown at level 0.525, step 1, values float32 > volume flip #57 Opened cryosparc_P4_J311_004_volume_map_sharp.mrc z flip as #58, grid size 80,80,80, pixel 3.32, shown at step 1, values float32 > close #57 > color #58 #fcedffff models > rename #58 CS_P4_J311_sharp_flip id #57 > save CS_P4_J311_sharp_flip.mrc #57 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260506_SA-F_B1_workflow.cxs"" > view P1 > hide #!57 models > hide #!56 models > show #!47 models > hide #!47 models > show #!48 models > save CS_P4_J302_NU_sharp.png supersample 3 transparentBackground true > hide #!48 models > show #!49 models > save CS_P4_J303_NU_sharp.png supersample 3 transparentBackground true > hide #!49 models > show #!50 models > save CS_P4_J304_NU_sharp.png supersample 3 transparentBackground true > hide #!50 models > show #!51 models > save CS_P4_J305_NU_sharp.png supersample 3 transparentBackground true > hide #!51 models > show #!52 models > volume #52 level 1.034 > save CS_P4_J306_NU_sharp.png supersample 3 transparentBackground true > hide #!52 models > show #!53 models > color #53 #fcedffff models > save CS_P4_J307_NU_sharp.png supersample 3 transparentBackground true > hide #!53 models > show #!54 models > save CS_P4_J308_NU_sharp.png supersample 3 transparentBackground true > hide #!54 models > show #!55 models > save CS_P4_J309_NU_sharp.png supersample 3 transparentBackground true > hide #!55 models > show #!56 models > volume #56 level 0.7192 > save CS_P4_J310_NU_sharp.png supersample 3 transparentBackground true > hide #!56 models > show #!57 models > save CS_P4_J311_NU_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260506_SA-F_B1_workflow.cxs"" ——— End of log from Wed May 6 15:19:28 2026 ——— > view name session-start opened ChimeraX session > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J323_006_volume_map_sharp.mrc"" Opened cryosparc_P4_J323_006_volume_map_sharp.mrc as #58, grid size 320,320,320, pixel 0.831, shown at level 0.0345, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J324_map_locres.mrc"" Opened cryosparc_P4_J324_map_locres.mrc as #59, grid size 320,320,320, pixel 0.831, shown at level 8.89, step 2, values float32 > hide #!57 models > hide #!58 models > show #!58 models > hide #!59 models > show #!59 models > volume flip #58 Opened cryosparc_P4_J323_006_volume_map_sharp.mrc z flip as #60, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #59 Opened cryosparc_P4_J324_map_locres.mrc z flip as #61, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #58 > close #59 > rename #60 CS_P4_J323_sharp_flip #58 Expected a keyword > rename #60 CS_P4_J323_sharp_flip id #58 > save CS_P4_J323_sharp_flip.mrc #58 > rename CS_P4_J324_map_locres_flip id #59 Missing or invalid ""models"" argument: invalid models specifier > rename #61 CS_P4_J324_map_locres_flip id #59 > save CS_P4_J324_map_locres_flip.mrc #59 > hide #!58 models > show #!58 models > hide #!59 models > volume #59 level 9.377 > hide #!59 models > volume #58 level 0.05889 > show #!59 models > volume #59 level 3.695 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow.cxs"" > ui tool show ""Surface Color"" > hide #!58 models > show #!58 models > hide #!59 models > color radial #58.1 palette #ffb17f:#4979d3:#99bfe5:#fff6c0:#f4fff3 > color sample #58.1 map #59 palette > 166.9,#ffb17f:198,#4979d3:229.1,#99bfe5:260.3,#fff6c0:291.4,#f4fff3 > outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.552, maximum 44.59 > color sample #58.1 map #59 palette > 2,#ffb17f:3,#4979d3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.552, maximum 44.59 > show #!59 models > hide #!58 models > hide #!59 models > show #!59 models > show #!58 models > hide #!59 models > show #!59 models > hide #!59 models > volume #58 level 0.0634 > volume #58 level 0.04264 > volume #58 level 0.07693 > volume #58 level 0.06069 > volume #58 level 0.07152 > volume #58 level 0.05889 > volume #58 level 0.05167 > volume #58 level 0.06159 > key #ffb17f:2 #4979d3:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > key pos 0.82265,0.196044 size 0.0692066,0.202924 > ui mousemode right translate > ui mousemode right ""color key"" > key pos 0.802943,0.231339 size 0.039822,0.144632 > key #ffb17f:2 #4979d3:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > key pos 0.836801,0.165731 size 0.0516869,0.238605 > show #41 models > key pos 0.820538,0.190547 size 0.0458442,0.242723 > save CS_P4_J323_sharp_flip.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow1.cxs"" > color sample #58.1 map #59 palette > 2,#ffb17f:3,#169bd3:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.532, maximum 44.61 > color sample #58.1 map #59 palette > 2,#ffb17f:3,#46c7f6:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.532, maximum 44.61 > color sample #58.1 map #59 palette > 2,#ffb17f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#f4fff3 outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.532, maximum 44.61 > key #ffb17f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #f4fff3:6 showTool true > ui mousemode right ""color key"" > color sample #58.1 map #59 palette > 2,#ffb17f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.532, maximum 44.61 > key #ffb17f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #ffb17f:6 showTool true > color sample #58.1 map #59 palette > 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.532, maximum 44.61 > key #13097f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #ffb17f:6 showTool true > save CS_P4_J323_sharp_flip2.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow2.cxs"" > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J329_005_volume_map_sharp.mrc"" Opened cryosparc_P4_J329_005_volume_map_sharp.mrc as #60, grid size 320,320,320, pixel 0.831, shown at level 0.0384, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J330_map_locres.mrc"" Opened cryosparc_P4_J330_map_locres.mrc as #61, grid size 320,320,320, pixel 0.831, shown at level 9.71, step 2, values float32 > hide #!58 models > hide #!60 models > show #!60 models > hide #!61 models > volume flip #60 Opened cryosparc_P4_J329_005_volume_map_sharp.mrc z flip as #62, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #61 Opened cryosparc_P4_J330_map_locres.mrc z flip as #63, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #60 > close #61 > rename #62 CS_P4_J329_sharp_flip id #60 > save CS_P4_J329_sharp_flip.mrc #60 > rename #63 rename > rename #63 CS_P4_J330_locres_flip id #61 > save CS_P4_J330_locres_flip.mrc #61 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow3.cxs"" > hide #!61 models > color sample #58.1 map #59 palette > 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080 Map values for surface ""surface"": minimum 2.944, mean 3.532, maximum 44.61 > color sample #60.1 map #61 palette > 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.466, maximum 46.71 > volume #60 level 0.06443 > key #13097f:2 #11b6e1:3 #99bfe5:4 #fff6c0:5 #ffb17f:6 showTool true > ui mousemode right ""color key"" > volume #60 level 0.05663 > save CS_P4_J329_locres_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow3.cxs"" ——— End of log from Thu May 7 15:58:17 2026 ——— > view name session-start opened ChimeraX session > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J300_005_volume_map_sharp.mrc"" Opened cryosparc_P4_J300_005_volume_map_sharp.mrc as #62, grid size 320,320,320, pixel 0.831, shown at level 0.0375, step 2, values float32 > open ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/cryosparc_P4_J301_map_locres.mrc"" Opened cryosparc_P4_J301_map_locres.mrc as #63, grid size 320,320,320, pixel 0.831, shown at level 9.68, step 2, values float32 > hide #!60 models > hide #!63 models > volume flip #62 Opened cryosparc_P4_J300_005_volume_map_sharp.mrc z flip as #64, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > volume flip #63 Opened cryosparc_P4_J301_map_locres.mrc z flip as #65, grid size 320,320,320, pixel 0.831, shown at step 1, values float32 > close #62 > close #63 > rename #64 CS_P4_J300_sharp_flip id #62 > save CS_P4_J300_sharp_flip.mrc #62 > rename #65 CS_P4_J301_locres_flip id #63 > save CS_P4_J301_locres_flip.mrc #63 > show #!46 models > show #!47 models > hide #!47 models > hide #!46 models > hide #!63 models > show #!63 models > volume #63 level 3.952 > hide #!63 models > volume #62 level 0.0392 > ui tool show ""Surface Color"" > color sample #62.1 map #63 palette #13097f:#11b6e1:#99bfe5:#fff6c0:#ffb17f > outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.383, maximum 43.37 > color sample #62.1 map #63 palette > 2,#13097f:3,#11b6e1:4,#99bfe5:5,#fff6c0:6,#ffb17f outsideColor #808080 Map values for surface ""surface"": minimum 0, mean 4.383, maximum 43.37 > show #!63 models > hide #!63 models > hide #!62 models > show #!62 models > volume #62 level 0.06614 > volume #62 level 0.05745 > save CS_P4_J300_locres_sharp.png supersample 3 transparentBackground true > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow4.cxs"" > open /Users/peiyuyu/Downloads/cryosparc_P7_J110_004_volume_map_sharp.mrc Opened cryosparc_P7_J110_004_volume_map_sharp.mrc as #64, grid size 160,160,160, pixel 1.66, shown at level 0.28, step 1, values float32 > hide #!62 models > close #64 > save ""/Users/peiyuyu/Documents/Goethe > University/2026/5_Manuscripts/1_AcrF/Figure/Figure_cryoEM_workflow/SA- > F_B1/20260507_SA-F_B1_workflow5.cxs"" ——— End of log from Thu May 7 21:11:39 2026 ——— > view name session-start opened ChimeraX session Failed to send bug report. Bug report server www.rbvi.ucsf.edu is unavailable [Repeated 1 time(s)] OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M4 Pro OpenGL vendor: Apple Python: 3.11.9 Locale: UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,8 Model Number: MX2F3D/A Chip: Apple M4 Pro Total Number of Cores: 14 (10 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.1 (24D70) Kernel Version: Darwin 24.3.0 Time since boot: 29天16小時42分鐘 Graphics/Displays: Apple M4 Pro: Chipset Model: Apple M4 Pro Type: GPU Bus: Built-In Total Number of Cores: 20 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LEN T22i-10: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.11 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.25.1 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 narwhals: 2.17.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 2.4.2 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 plotly: 6.5.2 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pyKVFinder: 0.9.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.2.5 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pytz: 2025.2 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.0.0 roman-numerals-py: 4.0.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.0.4 stack-data: 0.6.3 starlette: 0.50.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tomlkit: 0.14.0 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 tzdata: 2025.3 urllib3: 2.6.2 uvicorn: 0.38.0 wcwidth: 0.2.14 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect new normal Unassigned