id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16990 Crash moving window between screens milos.cvetkovic@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.1-x86_64-i386-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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: ""_segment.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 5269614592, ""size"" : 3915776, ""uuid"" : ""bfecdf7d-82ca-36af-86fb-90f272cdc263"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so"", ""name"" : ""etree.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 5221769216, ""size"" : 131072, ""uuid"" : ""21fc90fd-fbf7-3c7d-8a75-746218b81cb2"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so"", ""name"" : ""_elementpath.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 5741035520, ""size"" : 32768, ""uuid"" : ""65c46829-28f8-3e3d-8cdc-c208915d68a9"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so"", ""name"" : ""_graphics.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 5801410560, ""size"" : 32768, ""uuid"" : ""1989633c-45a1-31cf-8337-3d964444f286"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so"", ""name"" : ""_imagingmath.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703494725632, ""size"" : 245760, ""uuid"" : ""c214d771-f6a3-30be-b657-b4e0cb81c9df"", ""path"" : ""\/usr\/lib\/system\/libsystem_kernel.dylib"", ""name"" : ""libsystem_kernel.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703494971392, ""size"" : 49152, ""uuid"" : ""2b452c39-67e1-3f73-87ca-5e07d5f1e90d"", ""path"" : ""\/usr\/lib\/system\/libsystem_pthread.dylib"", ""name"" : ""libsystem_pthread.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703493554176, ""size"" : 561144, ""uuid"" : ""12e8dc9e-ee00-37e7-8830-dc84a6de23b1"", ""path"" : ""\/usr\/lib\/system\/libsystem_c.dylib"", ""name"" : ""libsystem_c.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703495204864, ""size"" : 40936, ""uuid"" : ""c55810b0-b8d2-3648-9009-570354c94d10"", ""path"" : ""\/usr\/lib\/system\/libsystem_platform.dylib"", ""name"" : ""libsystem_platform.dylib"" }, { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703694995456, ""CFBundleShortVersionString"" : ""19.0.0"", ""CFBundleIdentifier"" : ""com.apple.CoreImage"", ""size"" : 4300792, ""uuid"" : ""f377923c-3eb0-30fc-8a0e-5aab931d9da3"", ""path"" : ""\/System\/Library\/Frameworks\/CoreImage.framework\/Versions\/A\/CoreImage"", ""name"" : ""CoreImage"", ""CFBundleVersion"" : ""1510.80.3"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703555842048, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.AppKit"", ""size"" : 21999608, ""uuid"" : ""e3f76bb8-4950-3c7a-8aa7-8516a93aeeb9"", ""path"" : ""\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit"", ""name"" : ""AppKit"", ""CFBundleVersion"" : ""2575.40.6"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703491239936, ""size"" : 572544, ""uuid"" : ""f2913392-361a-304f-b30d-486be5639e2d"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" }, { ""source"" : ""P"", ""arch"" : ""x86_64h"", ""base"" : 140703495434240, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.CoreFoundation"", ""size"" : 4841443, ""uuid"" : ""404c409f-d28c-309d-ade3-f0ee6f1ca33d"", ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"", ""name"" : ""CoreFoundation"", ""CFBundleVersion"" : ""3302.1.400"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703512567808, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.Foundation"", ""size"" : 14880756, ""uuid"" : ""ff5888c8-5530-389a-b032-c6aa06e6d180"", ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"", ""name"" : ""Foundation"", ""CFBundleVersion"" : ""3302.1.400"" } ], ""sharedCache"" : { ""base"" : 140703490490368, ""size"" : 25769803776, ""uuid"" : ""5883cbf0-2a8e-3bdc-b903-9b0f91b0e9e4"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=5.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=5.0G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 148K 10 \nColorSync 256K 32 \nCoreAnimation 624K 87 \nCoreGraphics 16K 3 \nCoreUI image data 5224K 40 \nFoundation 16K 1 \nIOKit 23.3M 3 \nKernel Alloc Once 8K 1 \nMALLOC 4.0G 764 \nMALLOC guard page 48K 12 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 180K 45 \nStack 203.4M 46 \nStack Guard 56.0M 1 \nVM_ALLOCATE 405.7M 554 \nVM_ALLOCATE (reserved) 128.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 41.2M 1073 \n__DATA_CONST 114.1M 987 \n__DATA_DIRTY 2567K 338 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5176K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 215.7M 155 \n__OBJC_RO 76.9M 1 \n__OBJC_RW 2375K 2 \n__TEXT 1.4G 1094 \n__TPRO_CONST 272K 2 \ndyld private memory 40K 2 \nmapped file 232.9M 50 \nowned unmapped memory 201.5M 1 \nshared memory 3004K 28 \n=========== ======= ======= \nTOTAL 7.1G 5347 \nTOTAL, minus reserved VM space 6.9G 5347 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""6e9acb1c337fc953f556eb7d99f1f28e943ff976"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000021 }, { ""rolloutId"" : ""642da32dea3b2418c750f848"", ""factorPackIds"" : { ""VISUAL_INTELLIGENCE_VICTORIA"" : ""66d8b2f77cd4b62688efd2cf"" }, ""deploymentId"" : 240000004 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/cvetkom/Documents/chimera_sessions/20250228_post_polish_mix.cxs Opened cryosparc_P17_J1528_010_volume_map.mrc as #1, grid size 588,588,588, pixel 0.95, shown at level 0.0982, step 1, values float32 Opened J1741_class_00_00075_volume.mrc as #2, grid size 240,240,240, pixel 2.33, shown at level 0.296, step 1, values float32 Opened J1741_class_01_00075_volume.mrc as #3, grid size 240,240,240, pixel 2.33, shown at level 0.335, step 1, values float32 Opened J1741_class_02_00075_volume.mrc as #4, grid size 240,240,240, pixel 2.33, shown at level 0.377, step 1, values float32 Opened J1741_class_03_00075_volume.mrc as #5, grid size 240,240,240, pixel 2.33, shown at level 0.317, step 1, values float32 Opened J1741_class_04_00075_volume.mrc as #6, grid size 240,240,240, pixel 2.33, shown at level 0.466, step 1, values float32 Opened J1741_class_05_00075_volume.mrc as #7, grid size 240,240,240, pixel 2.33, shown at level 0.36, step 1, values float32 Opened J1741_class_06_00075_volume.mrc as #8, grid size 240,240,240, pixel 2.33, shown at level 0.295, step 1, values float32 Opened J1741_class_07_00075_volume.mrc as #9, grid size 240,240,240, pixel 2.33, shown at level 0.696, step 1, values float32 Opened J1745_class_00_00094_volume.mrc as #10, grid size 192,192,192, pixel 2.91, shown at level 0.451, step 1, values float32 Opened J1745_class_01_00094_volume.mrc as #11, grid size 192,192,192, pixel 2.91, shown at level 0.428, step 1, values float32 Opened J1745_class_02_00094_volume.mrc as #12, grid size 192,192,192, pixel 2.91, shown at level 0.526, step 1, values float32 Opened J1745_class_03_00094_volume.mrc as #13, grid size 192,192,192, pixel 2.91, shown at level 0.652, step 1, values float32 Opened J1745_class_04_00094_volume.mrc as #14, grid size 192,192,192, pixel 2.91, shown at level 15.3, step 1, values float32 Opened J1745_class_05_00094_volume.mrc as #15, grid size 192,192,192, pixel 2.91, shown at level 5.97, step 1, values float32 Opened cryosparc_P17_J1549_007_volume_map.mrc as #16, grid size 588,588,588, pixel 0.95, shown at level 0.1, step 1, values float32 Opened J1757_class_00_00039_volume.mrc as #17, grid size 120,120,120, pixel 4.65, shown at level 0.238, step 1, values float32 Opened J1757_class_01_00039_volume.mrc as #18, grid size 120,120,120, pixel 4.65, shown at level 0.232, step 1, values float32 Opened J1757_class_02_00039_volume.mrc as #19, grid size 120,120,120, pixel 4.65, shown at level 0.283, step 1, values float32 Opened J1757_class_03_00039_volume.mrc as #20, grid size 120,120,120, pixel 4.65, shown at level 0.348, step 1, values float32 Opened J1757_class_04_00039_volume.mrc as #21, grid size 120,120,120, pixel 4.65, shown at level 0.221, step 1, values float32 Opened J1757_class_05_00039_volume.mrc as #22, grid size 120,120,120, pixel 4.65, shown at level 0.341, step 1, values float32 Opened J1757_class_06_00039_volume.mrc as #23, grid size 120,120,120, pixel 4.65, shown at level 0.176, step 1, values float32 Opened J1757_class_07_00039_volume.mrc as #24, grid size 120,120,120, pixel 4.65, shown at level 0.311, step 1, values float32 Opened J1567_class_00_00061_volume.mrc as #25, grid size 120,120,120, pixel 4.65, shown at level 0.377, step 1, values float32 Opened J1567_class_01_00061_volume.mrc as #26, grid size 120,120,120, pixel 4.65, shown at level 0.297, step 1, values float32 Opened J1567_class_02_00061_volume.mrc as #27, grid size 120,120,120, pixel 4.65, shown at level 0.186, step 1, values float32 Opened J1567_class_03_00061_volume.mrc as #28, grid size 120,120,120, pixel 4.65, shown at level 0.33, step 1, values float32 Opened J1567_class_04_00061_volume.mrc as #29, grid size 120,120,120, pixel 4.65, shown at level 0.403, step 1, values float32 Opened cryosparc_P17_J1757_volume_map_consensus.mrc as #30, grid size 120,120,120, pixel 4.65, shown at level 0.168, step 1, values float32 Opened volume sum as #31, grid size 120,120,120, pixel 4.65, shown at level 0.5, step 1, values float32 Opened cryosparc_P17_J1757_volume_map_NCP_for_mask.mrc as #34, grid size 120,120,120, pixel 4.65, shown at level 0.5, step 1, values float32 Opened cryosparc_P17_J1765_mask.mrc as #33, grid size 120,120,120, pixel 4.65, shown at level 1, step 1, values float32 Opened run_it025_class001.mrc as #35, grid size 520,520,520, pixel 0.95, shown at level 0.00223, step 1, values float32 Opened run_it025_class002.mrc as #36, grid size 520,520,520, pixel 0.95, shown at level 0.00226, step 1, values float32 Opened run_it025_class003.mrc as #37, grid size 520,520,520, pixel 0.95, shown at level 0.00248, step 1, values float32 Opened run_it025_class004.mrc as #38, grid size 520,520,520, pixel 0.95, shown at level 0.0031, step 1, values float32 Opened run_it025_class001.mrc as #39, grid size 520,520,520, pixel 0.95, shown at level 0.00395, step 1, values float32 Opened run_it025_class002.mrc as #40, grid size 520,520,520, pixel 0.95, shown at level 0.0021, step 1, values float32 Opened run_it025_class003.mrc as #41, grid size 520,520,520, pixel 0.95, shown at level 0.00258, step 1, values float32 Opened run_it025_class004.mrc as #42, grid size 520,520,520, pixel 0.95, shown at level 0.00269, step 1, values float32 Opened run_it025_class005.mrc as #43, grid size 520,520,520, pixel 0.95, shown at level 0.0027, step 1, values float32 Opened run_it025_class006.mrc as #44, grid size 520,520,520, pixel 0.95, shown at level 0.00228, step 1, values float32 Opened run_it025_class001.mrc as #45, grid size 520,520,520, pixel 0.95, shown at level 0.00293, step 1, values float32 Opened run_it025_class002.mrc as #46, grid size 520,520,520, pixel 0.95, shown at level 0.00275, step 1, values float32 Opened run_it025_class003.mrc as #47, grid size 520,520,520, pixel 0.95, shown at level 0.00243, step 1, values float32 Opened run_it025_class004.mrc as #48, grid size 520,520,520, pixel 0.95, shown at level 0.00254, step 1, values float32 Opened run_it025_class005.mrc as #49, grid size 520,520,520, pixel 0.95, shown at level 0.00296, step 1, values float32 Opened run_it025_class002.mrc as #50, grid size 520,520,520, pixel 0.95, shown at level 0.00199, step 1, values float32 Opened run_it025_class006.mrc as #51, grid size 520,520,520, pixel 0.95, shown at level 0.00268, step 1, values float32 Opened run_it025_class001.mrc as #52, grid size 520,520,520, pixel 0.95, shown at level 0.00209, step 1, values float32 Opened run_it025_class004.mrc as #53, grid size 520,520,520, pixel 0.95, shown at level 0.00208, step 1, values float32 Opened run_it025_class002.mrc as #54, grid size 520,520,520, pixel 0.95, shown at level 0.00153, step 1, values float32 Opened cryosparc_P17_J1626_009_volume_map.mrc as #55, grid size 588,588,588, pixel 0.95, shown at level 0.0718, step 1, values float32 Opened cryosparc_P17_J1598_volume_map.mrc as #56, grid size 520,520,520, pixel 0.95, shown at level 0.0358, step 1, values float32 Opened cryosparc_P17_J1600_mask.mrc as #57, grid size 520,520,520, pixel 0.95, shown at level 0.799, step 1, values float32 Opened cryosparc_P17_J1762_008_volume_map.mrc as #58, grid size 588,588,588, pixel 0.95, shown at level 0.078, step 1, values float32 Opened cryosparc_P17_J1759_008_volume_map.mrc as #59, grid size 588,588,588, pixel 0.95, shown at level 0.12, step 1, values float32 Opened cryosparc_P17_J1760_007_volume_map.mrc as #60, grid size 588,588,588, pixel 0.95, shown at level 0.13, step 1, values float32 Opened cryosparc_P17_J1761_008_volume_map.mrc as #61, grid size 588,588,588, pixel 0.95, shown at level 0.14, step 1, values float32 Opened cryosparc_P17_J1748_008_volume_map.mrc as #62, grid size 588,588,588, pixel 0.95, shown at level 0.09, step 1, values float32 Opened cryosparc_P17_J1749_007_volume_map.mrc as #63, grid size 588,588,588, pixel 0.95, shown at level 0.09, step 1, values float32 Log from Fri Feb 28 11:55:25 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/cvetkom/Documents/chimera_sessions/20250227_ATPase_DNA_grip.cxs Opened cryosparc_P17_J1528_010_volume_map.mrc as #1, grid size 588,588,588, pixel 0.95, shown at level 0.0982, step 1, values float32 Opened J1741_class_00_00075_volume.mrc as #2, grid size 240,240,240, pixel 2.33, shown at level 0.296, step 1, values float32 Opened J1741_class_01_00075_volume.mrc as #3, grid size 240,240,240, pixel 2.33, shown at level 0.335, step 1, values float32 Opened J1741_class_02_00075_volume.mrc as #4, grid size 240,240,240, pixel 2.33, shown at level 0.377, step 1, values float32 Opened J1741_class_03_00075_volume.mrc as #5, grid size 240,240,240, pixel 2.33, shown at level 0.317, step 1, values float32 Opened J1741_class_04_00075_volume.mrc as #6, grid size 240,240,240, pixel 2.33, shown at level 0.466, step 1, values float32 Opened J1741_class_05_00075_volume.mrc as #7, grid size 240,240,240, pixel 2.33, shown at level 0.36, step 1, values float32 Opened J1741_class_06_00075_volume.mrc as #8, grid size 240,240,240, pixel 2.33, shown at level 0.295, step 1, values float32 Opened J1741_class_07_00075_volume.mrc as #9, grid size 240,240,240, pixel 2.33, shown at level 0.696, step 1, values float32 Opened J1745_class_00_00094_volume.mrc as #10, grid size 192,192,192, pixel 2.91, shown at level 0.451, step 1, values float32 Opened J1745_class_01_00094_volume.mrc as #11, grid size 192,192,192, pixel 2.91, shown at level 0.428, step 1, values float32 Opened J1745_class_02_00094_volume.mrc as #12, grid size 192,192,192, pixel 2.91, shown at level 0.526, step 1, values float32 Opened J1745_class_03_00094_volume.mrc as #13, grid size 192,192,192, pixel 2.91, shown at level 0.652, step 1, values float32 Opened J1745_class_04_00094_volume.mrc as #14, grid size 192,192,192, pixel 2.91, shown at level 15.3, step 1, values float32 Opened J1745_class_05_00094_volume.mrc as #15, grid size 192,192,192, pixel 2.91, shown at level 5.97, step 1, values float32 Log from Thu Feb 27 16:32:14 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/cvetkom/Documents/chimera_sessions/20250227_ATPase_DNA_grip.cxs Opened cryosparc_P17_J1528_010_volume_map.mrc as #1, grid size 588,588,588, pixel 0.95, shown at level 0.0982, step 1, values float32 Opened J1741_class_00_00075_volume.mrc as #2, grid size 240,240,240, pixel 2.33, shown at level 0.296, step 1, values float32 Opened J1741_class_01_00075_volume.mrc as #3, grid size 240,240,240, pixel 2.33, shown at level 0.335, step 1, values float32 Opened J1741_class_02_00075_volume.mrc as #4, grid size 240,240,240, pixel 2.33, shown at level 0.0857, step 1, values float32 Opened J1741_class_03_00075_volume.mrc as #5, grid size 240,240,240, pixel 2.33, shown at level 0.0673, step 1, values float32 Opened J1741_class_04_00075_volume.mrc as #6, grid size 240,240,240, pixel 2.33, shown at level 0.0974, step 1, values float32 Opened J1741_class_05_00075_volume.mrc as #7, grid size 240,240,240, pixel 2.33, shown at level 0.0705, step 1, values float32 Opened J1741_class_06_00075_volume.mrc as #8, grid size 240,240,240, pixel 2.33, shown at level 0.0727, step 1, values float32 Opened J1741_class_07_00075_volume.mrc as #9, grid size 240,240,240, pixel 2.33, shown at level 0.13, step 1, values float32 Opened J1745_class_00_00094_volume.mrc as #10, grid size 192,192,192, pixel 2.91, shown at level 0.103, step 1, values float32 Opened J1745_class_01_00094_volume.mrc as #11, grid size 192,192,192, pixel 2.91, shown at level 0.0878, step 1, values float32 Opened J1745_class_02_00094_volume.mrc as #12, grid size 192,192,192, pixel 2.91, shown at level 0.0973, step 1, values float32 Opened J1745_class_03_00094_volume.mrc as #13, grid size 192,192,192, pixel 2.91, shown at level 0.107, step 1, values float32 Opened J1745_class_04_00094_volume.mrc as #14, grid size 192,192,192, pixel 2.91, shown at level 13.4, step 1, values float32 Opened J1745_class_05_00094_volume.mrc as #15, grid size 192,192,192, pixel 2.91, shown at level 5.97, step 1, values float32 Log from Thu Feb 27 15:22:49 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class001.mrc Opened Cl3D_j581_run_it025_class001.mrc as #1, grid size 294,294,294, pixel 1.9, shown at level 0.0158, step 2, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class002.mrc Opened Cl3D_j581_run_it025_class002.mrc as #2, grid size 294,294,294, pixel 1.9, shown at level 0.0166, step 2, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class003.mrc Opened Cl3D_j581_run_it025_class003.mrc as #3, grid size 294,294,294, pixel 1.9, shown at level 0.0157, step 2, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class004.mrc Opened Cl3D_j581_run_it025_class004.mrc as #4, grid size 294,294,294, pixel 1.9, shown at level 0.0131, step 2, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class005.mrc Opened Cl3D_j581_run_it025_class005.mrc as #5, grid size 294,294,294, pixel 1.9, shown at level 0.013, step 2, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class006.mrc Opened Cl3D_j581_run_it025_class006.mrc as #6, grid size 294,294,294, pixel 1.9, shown at level 0.0154, step 2, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class007.mrc Opened Cl3D_j581_run_it025_class007.mrc as #7, grid size 294,294,294, pixel 1.9, shown at level 0.018, step 2, values float32 > tile 7 models tiled > tile 7 Expected a models specifier or a keyword > volume all step 1 > set bgColor white > lighting soft > lighting simple > volume #1 level 0.01308 > volume #2 level 0.01493 > volume #2 level 0.0143 > volume #3 level 0.01453 > volume #4 level 0.01256 > volume #5 level 0.01323 > volume #6 level 0.01418 > save /Users/cvetkom/Desktop/image3.png supersample 3 > close #1-7 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1528_010_volume_map.mrc Opened cryosparc_P17_J1528_010_volume_map.mrc as #1, grid size 588,588,588, pixel 0.95, shown at level 0.0454, step 4, values float32 > volume #1 step 1 > volume #1 level 0.0845 > volume #1 level 0.1119 > volume #1 level 0.09818 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_00_00075_volume.mrc Opened J1741_class_00_00075_volume.mrc as #2, grid size 240,240,240, pixel 2.33, shown at level 0.064, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_01_00075_volume.mrc Opened J1741_class_01_00075_volume.mrc as #3, grid size 240,240,240, pixel 2.33, shown at level 0.0741, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_02_00075_volume.mrc Opened J1741_class_02_00075_volume.mrc as #4, grid size 240,240,240, pixel 2.33, shown at level 0.0857, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_03_00075_volume.mrc Opened J1741_class_03_00075_volume.mrc as #5, grid size 240,240,240, pixel 2.33, shown at level 0.0673, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_04_00075_volume.mrc Opened J1741_class_04_00075_volume.mrc as #6, grid size 240,240,240, pixel 2.33, shown at level 0.0974, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_05_00075_volume.mrc Opened J1741_class_05_00075_volume.mrc as #7, grid size 240,240,240, pixel 2.33, shown at level 0.0705, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_06_00075_volume.mrc Opened J1741_class_06_00075_volume.mrc as #8, grid size 240,240,240, pixel 2.33, shown at level 0.0727, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_07_00075_volume.mrc Opened J1741_class_07_00075_volume.mrc as #9, grid size 240,240,240, pixel 2.33, shown at level 0.13, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_00_00094_volume.mrc Opened J1745_class_00_00094_volume.mrc as #10, grid size 192,192,192, pixel 2.91, shown at level 0.103, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_01_00094_volume.mrc Opened J1745_class_01_00094_volume.mrc as #11, grid size 192,192,192, pixel 2.91, shown at level 0.0878, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_02_00094_volume.mrc Opened J1745_class_02_00094_volume.mrc as #12, grid size 192,192,192, pixel 2.91, shown at level 0.0973, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_03_00094_volume.mrc Opened J1745_class_03_00094_volume.mrc as #13, grid size 192,192,192, pixel 2.91, shown at level 0.107, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_04_00094_volume.mrc Opened J1745_class_04_00094_volume.mrc as #14, grid size 192,192,192, pixel 2.91, shown at level 13.4, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_05_00094_volume.mrc Opened J1745_class_05_00094_volume.mrc as #15, grid size 192,192,192, pixel 2.91, shown at level 5.97, step 1, values float32 > volume all step 1 > hide #!15 models > hide #!14 models > hide #!13 models > hide #!12 models > hide #!11 models > hide #!10 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!5 models > hide #!6 models > hide #!4 models > hide #!3 models > show #!3 models > hide #!2 models > hide #!1 models > hide #!3 models > show #!2 models > volume #2 level 0.2493 > lighting soft > lighting simple > set bgColor black > set bgColor transparent > volume #2 level 0.2963 > volume #3 level 0.3843 > ui mousemode right zoom > volume #3 level 0.3973 > volume #3 level 0.3348 > show #!2 models > hide #!3 models > save /Users/cvetkom/Documents/chimera_sessions/20250227_ATPase_DNA_grip.cxs ——— End of log from Thu Feb 27 15:22:49 2025 ——— opened ChimeraX session > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > volume #4 level 0.387 > volume #4 level 0.3774 > volume #5 level 0.3801 > volume #5 level 0.2856 > volume #5 level 0.3318 > volume #5 level 0.3486 > volume #6 level 0.418 > lighting soft > lighting simple > volume #6 level 0.4659 > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!3 models > show #!3 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!3 models > hide #!6 models > show #!7 models > volume #7 level 0.3604 > volume #8 level 0.2682 > volume #8 level 0.2344 > volume #8 level 0.2947 > volume #9 level 0.6956 > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!5 models > volume #5 level 0.2877 > volume #5 level 0.3171 > volume #10 level 0.4639 > volume #10 level 0.4515 > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!10 models > show #!11 models > volume #11 level 0.4281 > volume #12 level 0.526 > volume #13 level 0.6189 > volume #13 level 0.6518 > volume #14 level 15.29 > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!6 models > show #!3 models > hide #!3 models > show #!3 models > hide #!6 models > show #!6 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > ui mousemode right zoom > save /Users/cvetkom/Documents/chimera_sessions/20250227_ATPase_DNA_grip.cxs ——— End of log from Thu Feb 27 16:32:14 2025 ——— opened ChimeraX session > hide #!6 models > show #!6 models > show #!2 models > hide #!6 models > show #!3 models > hide #!2 models > show #!6 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!6 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!7 models > hide #!7 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!3 models > hide #!3 models > show #!6 models > show #!3 models > hide #!6 models > show #!6 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!6 models > show #!4 models > hide #!4 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!11 models > hide #!11 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!13 models > show #!14 models > show #!15 models > hide #!15 models > hide #!14 models > hide #!13 models > show #!13 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > hide #!13 models > show #!10 models > show #!4 models > hide #!4 models > show #!4 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!4 models > show #!4 models > hide #!10 models > show #!10 models > hide #!10 models > show #!3 models > hide #!4 models > hide #!3 models > show #!3 models > show #!6 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!6 models > hide #!3 models > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1549_007_volume_map.mrc Opened cryosparc_P17_J1549_007_volume_map.mrc as #16, grid size 588,588,588, pixel 0.95, shown at level 0.0482, step 4, values float32 > volume #16 step 1 > volume #16 level 0.1686 > volume #16 level 0.1246 > volume #16 level 0.1093 > volume #16 level 0.1055 > volume #16 level 0.1 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_00_00039_volume.mrc Opened J1757_class_00_00039_volume.mrc as #17, grid size 120,120,120, pixel 4.65, shown at level 0.123, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_01_00039_volume.mrc Opened J1757_class_01_00039_volume.mrc as #18, grid size 120,120,120, pixel 4.65, shown at level 0.116, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_02_00039_volume.mrc Opened J1757_class_02_00039_volume.mrc as #19, grid size 120,120,120, pixel 4.65, shown at level 0.113, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_03_00039_volume.mrc Opened J1757_class_03_00039_volume.mrc as #20, grid size 120,120,120, pixel 4.65, shown at level 0.108, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_04_00039_volume.mrc Opened J1757_class_04_00039_volume.mrc as #21, grid size 120,120,120, pixel 4.65, shown at level 0.105, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_05_00039_volume.mrc Opened J1757_class_05_00039_volume.mrc as #22, grid size 120,120,120, pixel 4.65, shown at level 0.112, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_06_00039_volume.mrc Opened J1757_class_06_00039_volume.mrc as #23, grid size 120,120,120, pixel 4.65, shown at level 0.107, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_07_00039_volume.mrc Opened J1757_class_07_00039_volume.mrc as #24, grid size 120,120,120, pixel 4.65, shown at level 0.113, step 1, values float32 > hide #!18 models > hide #!19 models > hide #!20 models > hide #!21 models > hide #!22 models > hide #!23 models > hide #!24 models > volume #17 level 0.1994 > volume #17 level 0.2377 > volume #18 level 0.2399 > volume #18 level 0.2839 > volume #18 level 0.2324 > volume #19 level 0.2826 > show #!17 models > hide #!17 models > volume #20 level 0.348 > volume #21 level 0.2206 > volume #22 level 0.3406 > volume #23 level 0.1761 > volume #24 level 0.3109 > show #!21 models > hide #!21 models > show #!20 models > hide #!20 models > hide #!24 models > show #!22 models > show #!23 models > hide #!22 models > show #!22 models > show #!24 models > hide #!23 models > show #!21 models > hide #!21 models > show #!21 models > hide #!21 models > show #!21 models > hide #!21 models > show #!21 models > hide #!21 models > show #!20 models > hide #!20 models > show #!19 models > show #!18 models > show #!20 models > show #!21 models > show #!17 models > hide #!22 models > show #!22 models > hide #!16 models > show #!16 models > hide #!17 models > show #!17 models > hide #!17 models > hide #!19 models > hide #!18 models > show #!18 models > hide #!18 models > hide #!21 models > hide #!20 models > hide #!24 models > open > /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_00_00061_volume.mrc Opened J1567_class_00_00061_volume.mrc as #25, grid size 120,120,120, pixel 4.65, shown at level 0.103, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_01_00061_volume.mrc Opened J1567_class_01_00061_volume.mrc as #26, grid size 120,120,120, pixel 4.65, shown at level 0.107, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_02_00061_volume.mrc Opened J1567_class_02_00061_volume.mrc as #27, grid size 120,120,120, pixel 4.65, shown at level 0.105, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_03_00061_volume.mrc Opened J1567_class_03_00061_volume.mrc as #28, grid size 120,120,120, pixel 4.65, shown at level 0.116, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_04_00061_volume.mrc Opened J1567_class_04_00061_volume.mrc as #29, grid size 120,120,120, pixel 4.65, shown at level 0.103, step 1, values float32 > hide #!22 models > hide #!26 models > hide #!27 models > hide #!28 models > hide #!29 models > volume #25 level 0.2732 > volume #25 level 0.3769 > show #!26 models > hide #!25 models > volume #26 level 0.2965 > show #!25 models > hide #!25 models > hide #!26 models > show #!27 models > volume #27 level 0.1864 > volume #28 level 0.3188 > volume #28 level 0.3298 > volume #29 level 0.319 > volume #29 level 0.3859 > volume #29 level 0.4027 > open /Users/cvetkom/Downloads/cryosparc_P17_J1757_volume_map_consensus.mrc Opened cryosparc_P17_J1757_volume_map_consensus.mrc as #30, grid size 120,120,120, pixel 4.65, shown at level 0.136, step 1, values float32 > hide #!29 models > hide #!16 models > show #!16 models > volume #30 level 0.1682 > show #!17 models > show #!18 models > show #!19 models > show #!20 models > show #!21 models > show #!22 models > show #!23 models > hide #!22 models > hide #!17 models > hide #!18 models > hide #!19 models > hide #!20 models > hide #!21 models > hide #!23 models > show #!23 models > hide #!23 models > show #!24 models > hide #!24 models > show #!24 models > show #!23 models > hide #!23 models > show #!22 models > show #!21 models > hide #!22 models > show #!22 models > hide #!21 models > show #!21 models > show #!20 models > show #!19 models > show #!18 models > show #!17 models > volume add #17,18,19,20,21,22 Opened volume sum as #31, grid size 120,120,120, pixel 4.65, shown at step 1, values float32 > hide #!24 models > volume #31 level 0.5557 > volume #31 level 0.5367 > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!18 models > hide #!18 models > show #!18 models > hide #!18 models > show #!19 models > hide #!19 models > show #!20 models > hide #!20 models > show #!21 models > hide #!21 models > show #!22 models > hide #!22 models > show #!23 models > hide #!23 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > volume add #17,18,19,20,21,22 Opened volume sum as #32, grid size 120,120,120, pixel 4.65, shown at step 1, values float32 > close #32 > close #31 > show #!24 models > hide #!24 models > show #!24 models > show #!23 models > hide #!23 models > show #!22 models > show #!21 models > hide #!21 models > show #!21 models > show #!20 models > show #!19 models > show #!18 models > show #!17 models > volume add #17,18,19,20,21,22,24 Opened volume sum as #31, grid size 120,120,120, pixel 4.65, shown at step 1, values float32 > volume #31 level 0.585 > volume #31 level 0.5 > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!23 models > hide #!23 models > show #!24 models > show #!22 models > show #!21 models > show #!20 models > show #!19 models > show #!18 models > show #!17 models > hide #!24 models > show #!24 models > hide #!17 models > hide #!18 models > hide #!19 models > hide #!21 models > hide #!22 models > hide #!20 models > hide #!24 models > hide #!16 models > ui tool show ""Segment Map"" Segmenting volume sum, density threshold 0.500000 Showing 17 region surfaces 75 watershed regions, grouped to 17 regions Showing volume sum.seg - 17 regions, 17 surfaces > select #32.1 1 model selected Ungrouped to 2 regions > select #32.18 1 model selected Ungrouped to 2 regions > select #32.1 1 model selected Ungrouped to 2 regions > select #32.18 1 model selected Ungrouped to 2 regions > select #32.1 1 model selected Ungrouped to 2 regions > select #32.23 1 model selected Ungrouped to 2 regions > select #32.1 1 model selected Ungrouped to 2 regions > select #32.18 1 model selected Ungrouped to 2 regions > select #32.1 1 model selected Ungrouped to 2 regions > select #32.18 1 model selected Ungrouped to 2 regions > select #32.28 1 model selected Ungrouped to 2 regions > select #32.18 1 model selected Ungrouped to 0 regions > select #32.18 1 model selected Ungrouped to 0 regions > select #32.20 1 model selected Ungrouped to 2 regions > select #32.28 1 model selected Ungrouped to 2 regions > select #32.25 1 model selected Ungrouped to 2 regions > show #!17 models > show #!18 models > show #!19 models > hide #!19 models > hide #!18 models > hide #!17 models > show #!16 models > select #32.28 1 model selected Ungrouped to 2 regions > select #32.33 1 model selected Ungrouped to 0 regions > select #32.33 1 model selected Ungrouped to 0 regions > select #32.1 1 model selected > select add #32.27 2 models selected > select add #32.22 3 models selected > select add #32.21 4 models selected > select add #32.19 5 models selected > select add #32.25 6 models selected > select add #32.26 7 models selected Grouped 7 regions > select add #32.29 2 models selected > select add #32.18 3 models selected Grouped 3 regions > hide #!31 models > show #!29 models > hide #!29 models > show #!29 models > hide #!32 models > show #!32 models > hide #!29 models > show #!24 models > hide #!24 models > show #!24 models > hide #!32 models > show #!32 models > hide #!32 models > show #!32 models > hide #!32 models > show #!32 models > hide #!24 models > show #!23 models > hide #!23 models > show #!22 models > hide #!22 models > show #!21 models > hide #!21 models > show #!21 models > hide #!21 models > show #!20 models > hide #!20 models > show #!19 models > hide #!32 models > show #!32 models > hide #!19 models > show #!18 models > hide #!18 models > show #!17 models > hide #!17 models Showing 24 region surfaces > select #32.20 1 model selected Ungrouped to 2 regions > select #32.1 1 model selected > select add #32.19 2 models selected Grouped 2 regions Opened volume sum_imasked as #33, grid size 120,120,120, pixel 4.65, shown at step 1, values float32 > hide #!32 models > show #!32 models > hide #!32 models > show #!32 models > hide #!33 models > hide #!16 models > show #!24 models > show #!23 models > hide #!23 models > show #!22 models > show #!21 models > show #!20 models > show #!19 models > show #!18 models > show #!17 models > hide #!32 models > show #!32 models > hide #!32 models > show #!32 models > hide #!32 models > show #!32 models > hide #!24 models > hide #!22 models > hide #!21 models > hide #!20 models > hide #!19 models > hide #!18 models > hide #!17 models Showing 24 region surfaces > select #32.1 1 model selected Ungrouped to 2 regions > select #32.20 1 model selected Ungrouped to 3 regions > select #32.21 1 model selected Ungrouped to 0 regions > select #32.21 1 model selected Ungrouped to 0 regions > select #32.1 1 model selected Ungrouped to 7 regions > select #32.20 1 model selected > select #32.21 1 model selected Ungrouped to 0 regions > select #32.20 1 model selected Ungrouped to 2 regions > select #32.1 1 model selected Ungrouped to 2 regions > select #32.20 1 model selected Ungrouped to 2 regions > select #32.37 1 model selected Ungrouped to 0 regions > select #32.37 1 model selected Ungrouped to 0 regions > select #32.21 1 model selected Ungrouped to 0 regions > hide #!32 models > show #!33 models > ui mousemode right ""map eraser"" > volume erase #33 center 232.01,334.59,191.4 radius 158.31 > show #!16 models > ui tool show ""Map Filter"" > volume gaussian #33 sDev 1.21 Opened volume sum_imasked gaussian as #34, grid size 120,120,120, pixel 4.65, shown at step 1, values float32 > close #34 > volume gaussian #33 sDev 2 Opened volume sum_imasked gaussian as #34, grid size 120,120,120, pixel 4.65, shown at step 1, values float32 > close #33 > volume #34 level 0.5 > ui mousemode right zoom > save > /Users/cvetkom/Downloads/cryosparc_P17_J1757_volume_map_NCP_for_mask.mrc > models #34 > open /Users/cvetkom/Downloads/cryosparc_P17_J1765_mask.mrc Opened cryosparc_P17_J1765_mask.mrc as #33, grid size 120,120,120, pixel 4.65, shown at level 1, step 1, values float32 > volume #33 level 1 > volume #33 color #ffffb27d > volume #33 level 0.5139 > volume #33 level 1 > hide #!34 models > hide #!33 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!18 models > hide #!18 models > show #!19 models > hide #!19 models > show #!20 models > hide #!20 models > show #!21 models > hide #!21 models > show #!22 models > hide #!22 models > show #!23 models > hide #!23 models > show #!24 models > hide #!24 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1479/run_it025_class001.mrc Opened run_it025_class001.mrc as #35, grid size 520,520,520, pixel 0.95, shown at level 0.000296, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1479/run_it025_class002.mrc Opened run_it025_class002.mrc as #36, grid size 520,520,520, pixel 0.95, shown at level 0.000188, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1479/run_it025_class003.mrc Opened run_it025_class003.mrc as #37, grid size 520,520,520, pixel 0.95, shown at level 0.000293, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1479/run_it025_class004.mrc Opened run_it025_class004.mrc as #38, grid size 520,520,520, pixel 0.95, shown at level 0.000144, step 4, values float32 > hide #!16 models > hide #!23 models > volume all step 1 > volume #35 level 0.00175 > volume #35 level 0.001985 > volume #36 level 0.001419 > volume #36 level 0.002258 > volume #35 level 0.002231 > volume #37 level 0.001461 > volume #37 level 0.002052 > volume #38 level 0.003347 > volume #38 level 0.003643 > volume #38 level 0.003021 > volume #38 level 0.002881 > volume #38 level 0.003099 > volume #37 level 0.002479 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class001.mrc Opened run_it025_class001.mrc as #39, grid size 520,520,520, pixel 0.95, shown at level 0.000136, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class002.mrc Opened run_it025_class002.mrc as #40, grid size 520,520,520, pixel 0.95, shown at level 0.000382, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class003.mrc Opened run_it025_class003.mrc as #41, grid size 520,520,520, pixel 0.95, shown at level 0.000168, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class004.mrc Opened run_it025_class004.mrc as #42, grid size 520,520,520, pixel 0.95, shown at level 0.000171, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class005.mrc Opened run_it025_class005.mrc as #43, grid size 520,520,520, pixel 0.95, shown at level 0.000178, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class006.mrc Opened run_it025_class006.mrc as #44, grid size 520,520,520, pixel 0.95, shown at level 0.000256, step 4, values float32 > volume all step 1 > volume #39 level 0.003951 > volume #40 level 0.002104 > volume #41 level 0.000915 > volume #41 level 0.002577 > volume #42 level 0.002549 > volume #42 level 0.00269 > volume #43 level 0.001448 > volume #43 level 0.002702 > volume #44 level 0.002278 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class001.mrc Opened run_it025_class001.mrc as #45, grid size 520,520,520, pixel 0.95, shown at level 0.00022, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class002.mrc Opened run_it025_class002.mrc as #46, grid size 520,520,520, pixel 0.95, shown at level 0.000144, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class003.mrc Opened run_it025_class003.mrc as #47, grid size 520,520,520, pixel 0.95, shown at level 0.000205, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class004.mrc Opened run_it025_class004.mrc as #48, grid size 520,520,520, pixel 0.95, shown at level 0.00024, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class005.mrc Opened run_it025_class005.mrc as #49, grid size 520,520,520, pixel 0.95, shown at level 0.000309, step 4, values float32 > volume all step 1 > volume #45 level 0.002525 > volume #45 level 0.002927 > volume #46 level 0.002752 > volume #47 level 0.002429 > volume #48 level 0.002541 > volume #49 level 0.002957 > show #!49 models > hide #!49 models > show #!48 models > hide #!48 models > show #!47 models > hide #!47 models > show #!49 models > hide #!49 models > volume #46 level 0.002752 > hide #!36 models > show #!36 models > show #!38 models > hide #!36 models > hide #!38 models > show #!36 models > hide #!36 models > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1476/run_it025_class002.mrc Opened run_it025_class002.mrc as #50, grid size 520,520,520, pixel 0.95, shown at level 0.000201, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1476/run_it025_class006.mrc Opened run_it025_class006.mrc as #51, grid size 520,520,520, pixel 0.95, shown at level 0.000132, step 4, values float32 > volume all step 1 > volume #50 level 0.002655 > volume #50 level 0.002444 > volume #51 level 0.002852 > volume #50 level 0.001989 > volume #51 level 0.002679 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1475/run_it025_class001.mrc Opened run_it025_class001.mrc as #52, grid size 520,520,520, pixel 0.95, shown at level 0.000198, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1475/run_it025_class004.mrc Opened run_it025_class004.mrc as #53, grid size 520,520,520, pixel 0.95, shown at level 0.00011, step 4, values float32 > volume all step 1 > volume #52 level 0.00258 > volume #52 level 0.002524 > volume #53 level 0.002425 > volume #52 level 0.002093 > volume #53 level 0.002078 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1474/run_it025_class002.mrc Opened run_it025_class002.mrc as #54, grid size 520,520,520, pixel 0.95, shown at level 0.00018, step 4, values float32 > volume all step 1 > volume #54 level 0.002427 > volume #54 level 0.001525 > open /Users/cvetkom/Downloads/cryosparc_P17_J1626_009_volume_map.mrc Opened cryosparc_P17_J1626_009_volume_map.mrc as #55, grid size 588,588,588, pixel 0.95, shown at level 0.0688, step 4, values float32 > volume #55 step 1 > lighting soft > volume #55 level 0.07079 > volume #55 level 0.09629 > volume #55 level 0.07181 > hide #!55 models > show #!36 models > lighting simple [Repeated 1 time(s)] > show #!42 models > hide #!36 models > show #!36 models > hide #!36 models > show #!36 models > hide #!36 models > hide #!42 models > open /Users/cvetkom/Downloads/cryosparc_P17_J1598_volume_map.mrc Opened cryosparc_P17_J1598_volume_map.mrc as #56, grid size 520,520,520, pixel 0.95, shown at level 0.00289, step 4, values float32 > open /Users/cvetkom/Downloads/cryosparc_P17_J1600_mask.mrc Opened cryosparc_P17_J1600_mask.mrc as #57, grid size 520,520,520, pixel 0.95, shown at level 0.799, step 4, values float32 > hide #!56 models > show #!56 models > volume #56 level 0.03581 > volume #56 step 1 > volume #57 color #ffb2ff82 > volume #57 step 1 > open /Users/cvetkom/Downloads/cryosparc_P17_J1762_008_volume_map.mrc Opened cryosparc_P17_J1762_008_volume_map.mrc as #58, grid size 588,588,588, pixel 0.95, shown at level 0.061, step 4, values float32 > volume #58 step 1 > volume #58 level 0.09631 > volume #58 level 0.07799 > lighting soft > open /Users/cvetkom/Downloads/cryosparc_P17_J1759_008_volume_map.mrc Opened cryosparc_P17_J1759_008_volume_map.mrc as #59, grid size 588,588,588, pixel 0.95, shown at level 0.0499, step 4, values float32 > hide #!58 models > volume #59 step 1 > volume #59 level 0.1244 > lighting simple > volume #59 level 0.1026 > ui tool show ""Side View"" > volume #59 level 0.1135 > lighting soft > lighting full > lighting simple > open /Users/cvetkom/Downloads/cryosparc_P17_J1760_007_volume_map.mrc Opened cryosparc_P17_J1760_007_volume_map.mrc as #60, grid size 588,588,588, pixel 0.95, shown at level 0.047, step 4, values float32 > open /Users/cvetkom/Downloads/cryosparc_P17_J1761_008_volume_map.mrc Opened cryosparc_P17_J1761_008_volume_map.mrc as #61, grid size 588,588,588, pixel 0.95, shown at level 0.0467, step 4, values float32 > volume #60 step 1 > volume #61 step 1 > volume #60 level 0.1558 > volume #60 level 0.1281 > volume #61 level 0.1442 > open /Users/cvetkom/Downloads/cryosparc_P17_J1748_008_volume_map.mrc Opened cryosparc_P17_J1748_008_volume_map.mrc as #62, grid size 588,588,588, pixel 0.95, shown at level 0.0485, step 4, values float32 > open /Users/cvetkom/Downloads/cryosparc_P17_J1749_007_volume_map.mrc Opened cryosparc_P17_J1749_007_volume_map.mrc as #63, grid size 588,588,588, pixel 0.95, shown at level 0.048, step 4, values float32 > volume #62 step 2 > volume #62 step 1 > volume #63 step 1 > volume #62 level 0.1539 > volume #63 level 0.1446 > volume #62 color darkgrey [Repeated 1 time(s)] > volume #62 color #929292 > volume #62 color darkgrey > volume #62 color #929292 > volume #60 level 0.13 > volume #62 level 0.13 > volume #62 level 0.135 > volume #62 level 0.14 > volume #61 level 0.14 > volume #63 level 0.14 > show #!59 models > hide #!62 models > volume #59 color #009193 > volume #59 level 0.13 > volume #59 level 0.12 > lighting soft [Repeated 1 time(s)] > lighting simple > hide #!59 models > show #!62 models > show #!63 models > hide #!62 models > show #!62 models > hide #!63 models > hide #!62 models > show #!59 models > show #!62 models > hide #!62 models > show #!63 models > hide #!59 models > show #!59 models > hide #!63 models > show #!63 models > hide #!63 models > hide #!59 models > show #!60 models > show #!62 models > hide #!62 models > show #!61 models > hide #!61 models > show #!61 models > hide #!60 models > show #!60 models > hide #!61 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!60 models > show #!60 models > hide #!60 models > hide #!62 models > show #!61 models > show #!63 models > hide #!63 models > show #!63 models > hide #!63 models > show #!63 models > hide #!63 models > show #!63 models > hide #!63 models > show #!63 models > hide #!63 models > hide #!61 models > show #!62 models > volume #63 level 0.1 > volume #63 level 0.06 > volume #63 level 0.08 > volume #63 level 0.085 > volume #63 level 0.09 > volume #62 level 0.09 > show #!63 models > hide #!62 models > show #!62 models > hide #!63 models > show #!63 models > hide #!63 models > show #!63 models > hide #!63 models > show #!63 models > hide #!63 models > hide #!62 models > show #!62 models > show #!63 models > save /Users/cvetkom/Documents/chimera_sessions/20250228_post_polish_mix.cxs ——— End of log from Fri Feb 28 11:55:25 2025 ——— opened ChimeraX session Showing volume sum.seg - 36 regions, 36 surfaces > ui tool show ""Side View"" > view > hide #!32 models > open > /Users/cvetkom/Downloads/cryosparc_P17_J1773_00025_volume_series/J1773_class_00_00025_volume.mrc Opened J1773_class_00_00025_volume.mrc as #64, grid size 240,240,240, pixel 2.33, shown at level 0.044, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1773_00025_volume_series/J1773_class_01_00025_volume.mrc Opened J1773_class_01_00025_volume.mrc as #65, grid size 240,240,240, pixel 2.33, shown at level 0.0477, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1773_00025_volume_series/J1773_class_02_00025_volume.mrc Opened J1773_class_02_00025_volume.mrc as #66, grid size 240,240,240, pixel 2.33, shown at level 0.0524, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1773_00025_volume_series/J1773_class_03_00025_volume.mrc Opened J1773_class_03_00025_volume.mrc as #67, grid size 240,240,240, pixel 2.33, shown at level 0.0544, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1773_00025_volume_series/J1773_class_04_00025_volume.mrc Opened J1773_class_04_00025_volume.mrc as #68, grid size 240,240,240, pixel 2.33, shown at level 0.0557, step 1, values float32 > volume #62 level 0.09192 > volume #64 level 0.04924 > volume #65 level 0.0645 > volume #67 level 0.06256 > volume #66 level 0.1228 > volume #66 level 0.1066 > volume #67 level 0.08881 > volume #68 level 0.1067 > volume #68 level 0.111 > volume #67 level 0.1008 > volume #67 level 0.1074 > volume #65 level 0.09522 > hide #!62 models > show #!63 models > open > /Users/cvetkom/Downloads/cryosparc_P17_J1776_00024_volume_series/J1776_class_00_00024_volume.mrc Opened J1776_class_00_00024_volume.mrc as #69, grid size 240,240,240, pixel 2.33, shown at level 0.0548, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1776_00024_volume_series/J1776_class_01_00024_volume.mrc Opened J1776_class_01_00024_volume.mrc as #70, grid size 240,240,240, pixel 2.33, shown at level 0.0405, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1776_00024_volume_series/J1776_class_02_00024_volume.mrc Opened J1776_class_02_00024_volume.mrc as #71, grid size 240,240,240, pixel 2.33, shown at level 0.0456, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1776_00024_volume_series/J1776_class_03_00024_volume.mrc Opened J1776_class_03_00024_volume.mrc as #72, grid size 240,240,240, pixel 2.33, shown at level 0.0499, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1776_00024_volume_series/J1776_class_04_00024_volume.mrc Opened J1776_class_04_00024_volume.mrc as #73, grid size 240,240,240, pixel 2.33, shown at level 0.0493, step 1, values float32 > volume #69 level 0.1114 > volume #69 level 0.115 > volume #70 level 0.1081 > volume #71 level 0.09332 > volume #72 level 0.1059 > volume #73 level 0.09531 > volume #73 level 0.09973 > volume #73 level 0.09807 > hide #!63 models > show #!63 models > hide #!63 models > show #!16 models > open > /Users/cvetkom/Downloads/cryosparc_P17_J1766_00039_volume_series/J1766_class_00_00039_volume.mrc Opened J1766_class_00_00039_volume.mrc as #74, grid size 120,120,120, pixel 4.65, shown at level 0.11, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1766_00039_volume_series/J1766_class_01_00039_volume.mrc Opened J1766_class_01_00039_volume.mrc as #75, grid size 120,120,120, pixel 4.65, shown at level 0.121, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1766_00039_volume_series/J1766_class_02_00039_volume.mrc Opened J1766_class_02_00039_volume.mrc as #76, grid size 120,120,120, pixel 4.65, shown at level 0.107, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1766_00039_volume_series/J1766_class_03_00039_volume.mrc Opened J1766_class_03_00039_volume.mrc as #77, grid size 120,120,120, pixel 4.65, shown at level 0.0991, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1766_00039_volume_series/J1766_class_04_00039_volume.mrc Opened J1766_class_04_00039_volume.mrc as #78, grid size 120,120,120, pixel 4.65, shown at level 0.0987, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1766_00039_volume_series/J1766_class_05_00039_volume.mrc Opened J1766_class_05_00039_volume.mrc as #79, grid size 120,120,120, pixel 4.65, shown at level 0.105, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1766_00039_volume_series/J1766_class_06_00039_volume.mrc Opened J1766_class_06_00039_volume.mrc as #80, grid size 120,120,120, pixel 4.65, shown at level 0.0997, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1766_00039_volume_series/J1766_class_07_00039_volume.mrc Opened J1766_class_07_00039_volume.mrc as #81, grid size 120,120,120, pixel 4.65, shown at level 0.105, step 1, values float32 > hide #!74 models > hide #!81 models > show #!74 models > volume #74 level 0.227 > volume #75 level 0.2227 > volume #75 level 0.2711 > volume #76 level 0.3119 > volume #77 level 0.3586 > volume #77 level 0.2851 > volume #78 level 0.2774 > volume #78 level 0.2938 > volume #79 level 0.3079 > volume #79 level 0.3271 > volume #80 level 0.3116 > volume #81 level 0.3244 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/cvetkom/Documents/chimera_sessions/20250228_post_polish_mix.cxs Opened cryosparc_P17_J1528_010_volume_map.mrc as #1, grid size 588,588,588, pixel 0.95, shown at level 0.0982, step 1, values float32 Opened J1741_class_00_00075_volume.mrc as #2, grid size 240,240,240, pixel 2.33, shown at level 0.296, step 1, values float32 Opened J1741_class_01_00075_volume.mrc as #3, grid size 240,240,240, pixel 2.33, shown at level 0.335, step 1, values float32 Opened J1741_class_02_00075_volume.mrc as #4, grid size 240,240,240, pixel 2.33, shown at level 0.377, step 1, values float32 Opened J1741_class_03_00075_volume.mrc as #5, grid size 240,240,240, pixel 2.33, shown at level 0.317, step 1, values float32 Opened J1741_class_04_00075_volume.mrc as #6, grid size 240,240,240, pixel 2.33, shown at level 0.466, step 1, values float32 Opened J1741_class_05_00075_volume.mrc as #7, grid size 240,240,240, pixel 2.33, shown at level 0.36, step 1, values float32 Opened J1741_class_06_00075_volume.mrc as #8, grid size 240,240,240, pixel 2.33, shown at level 0.295, step 1, values float32 Opened J1741_class_07_00075_volume.mrc as #9, grid size 240,240,240, pixel 2.33, shown at level 0.696, step 1, values float32 Opened J1745_class_00_00094_volume.mrc as #10, grid size 192,192,192, pixel 2.91, shown at level 0.451, step 1, values float32 Opened J1745_class_01_00094_volume.mrc as #11, grid size 192,192,192, pixel 2.91, shown at level 0.428, step 1, values float32 Opened J1745_class_02_00094_volume.mrc as #12, grid size 192,192,192, pixel 2.91, shown at level 0.526, step 1, values float32 Opened J1745_class_03_00094_volume.mrc as #13, grid size 192,192,192, pixel 2.91, shown at level 0.652, step 1, values float32 Opened J1745_class_04_00094_volume.mrc as #14, grid size 192,192,192, pixel 2.91, shown at level 15.3, step 1, values float32 Opened J1745_class_05_00094_volume.mrc as #15, grid size 192,192,192, pixel 2.91, shown at level 5.97, step 1, values float32 Opened cryosparc_P17_J1549_007_volume_map.mrc as #16, grid size 588,588,588, pixel 0.95, shown at level 0.1, step 1, values float32 Opened J1757_class_00_00039_volume.mrc as #17, grid size 120,120,120, pixel 4.65, shown at level 0.238, step 1, values float32 Opened J1757_class_01_00039_volume.mrc as #18, grid size 120,120,120, pixel 4.65, shown at level 0.232, step 1, values float32 Opened J1757_class_02_00039_volume.mrc as #19, grid size 120,120,120, pixel 4.65, shown at level 0.283, step 1, values float32 Opened J1757_class_03_00039_volume.mrc as #20, grid size 120,120,120, pixel 4.65, shown at level 0.348, step 1, values float32 Opened J1757_class_04_00039_volume.mrc as #21, grid size 120,120,120, pixel 4.65, shown at level 0.221, step 1, values float32 Opened J1757_class_05_00039_volume.mrc as #22, grid size 120,120,120, pixel 4.65, shown at level 0.341, step 1, values float32 Opened J1757_class_06_00039_volume.mrc as #23, grid size 120,120,120, pixel 4.65, shown at level 0.176, step 1, values float32 Opened J1757_class_07_00039_volume.mrc as #24, grid size 120,120,120, pixel 4.65, shown at level 0.311, step 1, values float32 Opened J1567_class_00_00061_volume.mrc as #25, grid size 120,120,120, pixel 4.65, shown at level 0.377, step 1, values float32 Opened J1567_class_01_00061_volume.mrc as #26, grid size 120,120,120, pixel 4.65, shown at level 0.297, step 1, values float32 Opened J1567_class_02_00061_volume.mrc as #27, grid size 120,120,120, pixel 4.65, shown at level 0.186, step 1, values float32 Opened J1567_class_03_00061_volume.mrc as #28, grid size 120,120,120, pixel 4.65, shown at level 0.33, step 1, values float32 Opened J1567_class_04_00061_volume.mrc as #29, grid size 120,120,120, pixel 4.65, shown at level 0.403, step 1, values float32 Opened cryosparc_P17_J1757_volume_map_consensus.mrc as #30, grid size 120,120,120, pixel 4.65, shown at level 0.168, step 1, values float32 Opened volume sum as #31, grid size 120,120,120, pixel 4.65, shown at level 0.5, step 1, values float32 Opened cryosparc_P17_J1757_volume_map_NCP_for_mask.mrc as #34, grid size 120,120,120, pixel 4.65, shown at level 0.5, step 1, values float32 Opened cryosparc_P17_J1765_mask.mrc as #33, grid size 120,120,120, pixel 4.65, shown at level 1, step 1, values float32 Opened run_it025_class001.mrc as #35, grid size 520,520,520, pixel 0.95, shown at level 0.00223, step 1, values float32 Opened run_it025_class002.mrc as #36, grid size 520,520,520, pixel 0.95, shown at level 0.00226, step 1, values float32 Opened run_it025_class003.mrc as #37, grid size 520,520,520, pixel 0.95, shown at level 0.00248, step 1, values float32 Opened run_it025_class004.mrc as #38, grid size 520,520,520, pixel 0.95, shown at level 0.0031, step 1, values float32 Opened run_it025_class001.mrc as #39, grid size 520,520,520, pixel 0.95, shown at level 0.00395, step 1, values float32 Opened run_it025_class002.mrc as #40, grid size 520,520,520, pixel 0.95, shown at level 0.0021, step 1, values float32 Opened run_it025_class003.mrc as #41, grid size 520,520,520, pixel 0.95, shown at level 0.00258, step 1, values float32 Opened run_it025_class004.mrc as #42, grid size 520,520,520, pixel 0.95, shown at level 0.00269, step 1, values float32 Opened run_it025_class005.mrc as #43, grid size 520,520,520, pixel 0.95, shown at level 0.0027, step 1, values float32 Opened run_it025_class006.mrc as #44, grid size 520,520,520, pixel 0.95, shown at level 0.00228, step 1, values float32 Opened run_it025_class001.mrc as #45, grid size 520,520,520, pixel 0.95, shown at level 0.00293, step 1, values float32 Opened run_it025_class002.mrc as #46, grid size 520,520,520, pixel 0.95, shown at level 0.00275, step 1, values float32 Opened run_it025_class003.mrc as #47, grid size 520,520,520, pixel 0.95, shown at level 0.00243, step 1, values float32 Opened run_it025_class004.mrc as #48, grid size 520,520,520, pixel 0.95, shown at level 0.00254, step 1, values float32 Opened run_it025_class005.mrc as #49, grid size 520,520,520, pixel 0.95, shown at level 0.00296, step 1, values float32 Opened run_it025_class002.mrc as #50, grid size 520,520,520, pixel 0.95, shown at level 0.00199, step 1, values float32 Opened run_it025_class006.mrc as #51, grid size 520,520,520, pixel 0.95, shown at level 0.00268, step 1, values float32 Opened run_it025_class001.mrc as #52, grid size 520,520,520, pixel 0.95, shown at level 0.00209, step 1, values float32 Opened run_it025_class004.mrc as #53, grid size 520,520,520, pixel 0.95, shown at level 0.00208, step 1, values float32 Opened run_it025_class002.mrc as #54, grid size 520,520,520, pixel 0.95, shown at level 0.00153, step 1, values float32 Opened cryosparc_P17_J1626_009_volume_map.mrc as #55, grid size 588,588,588, pixel 0.95, shown at level 0.0718, step 1, values float32 Opened cryosparc_P17_J1598_volume_map.mrc as #56, grid size 520,520,520, pixel 0.95, shown at level 0.0358, step 1, values float32 Opened cryosparc_P17_J1600_mask.mrc as #57, grid size 520,520,520, pixel 0.95, shown at level 0.799, step 1, values float32 Opened cryosparc_P17_J1762_008_volume_map.mrc as #58, grid size 588,588,588, pixel 0.95, shown at level 0.078, step 1, values float32 Opened cryosparc_P17_J1759_008_volume_map.mrc as #59, grid size 588,588,588, pixel 0.95, shown at level 0.12, step 1, values float32 Opened cryosparc_P17_J1760_007_volume_map.mrc as #60, grid size 588,588,588, pixel 0.95, shown at level 0.13, step 1, values float32 Opened cryosparc_P17_J1761_008_volume_map.mrc as #61, grid size 588,588,588, pixel 0.95, shown at level 0.14, step 1, values float32 Opened cryosparc_P17_J1748_008_volume_map.mrc as #62, grid size 588,588,588, pixel 0.95, shown at level 0.09, step 1, values float32 Opened cryosparc_P17_J1749_007_volume_map.mrc as #63, grid size 588,588,588, pixel 0.95, shown at level 0.09, step 1, values float32 Log from Fri Feb 28 11:55:25 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/cvetkom/Documents/chimera_sessions/20250227_ATPase_DNA_grip.cxs Opened cryosparc_P17_J1528_010_volume_map.mrc as #1, grid size 588,588,588, pixel 0.95, shown at level 0.0982, step 1, values float32 Opened J1741_class_00_00075_volume.mrc as #2, grid size 240,240,240, pixel 2.33, shown at level 0.296, step 1, values float32 Opened J1741_class_01_00075_volume.mrc as #3, grid size 240,240,240, pixel 2.33, shown at level 0.335, step 1, values float32 Opened J1741_class_02_00075_volume.mrc as #4, grid size 240,240,240, pixel 2.33, shown at level 0.377, step 1, values float32 Opened J1741_class_03_00075_volume.mrc as #5, grid size 240,240,240, pixel 2.33, shown at level 0.317, step 1, values float32 Opened J1741_class_04_00075_volume.mrc as #6, grid size 240,240,240, pixel 2.33, shown at level 0.466, step 1, values float32 Opened J1741_class_05_00075_volume.mrc as #7, grid size 240,240,240, pixel 2.33, shown at level 0.36, step 1, values float32 Opened J1741_class_06_00075_volume.mrc as #8, grid size 240,240,240, pixel 2.33, shown at level 0.295, step 1, values float32 Opened J1741_class_07_00075_volume.mrc as #9, grid size 240,240,240, pixel 2.33, shown at level 0.696, step 1, values float32 Opened J1745_class_00_00094_volume.mrc as #10, grid size 192,192,192, pixel 2.91, shown at level 0.451, step 1, values float32 Opened J1745_class_01_00094_volume.mrc as #11, grid size 192,192,192, pixel 2.91, shown at level 0.428, step 1, values float32 Opened J1745_class_02_00094_volume.mrc as #12, grid size 192,192,192, pixel 2.91, shown at level 0.526, step 1, values float32 Opened J1745_class_03_00094_volume.mrc as #13, grid size 192,192,192, pixel 2.91, shown at level 0.652, step 1, values float32 Opened J1745_class_04_00094_volume.mrc as #14, grid size 192,192,192, pixel 2.91, shown at level 15.3, step 1, values float32 Opened J1745_class_05_00094_volume.mrc as #15, grid size 192,192,192, pixel 2.91, shown at level 5.97, step 1, values float32 Log from Thu Feb 27 16:32:14 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/cvetkom/Documents/chimera_sessions/20250227_ATPase_DNA_grip.cxs Opened cryosparc_P17_J1528_010_volume_map.mrc as #1, grid size 588,588,588, pixel 0.95, shown at level 0.0982, step 1, values float32 Opened J1741_class_00_00075_volume.mrc as #2, grid size 240,240,240, pixel 2.33, shown at level 0.296, step 1, values float32 Opened J1741_class_01_00075_volume.mrc as #3, grid size 240,240,240, pixel 2.33, shown at level 0.335, step 1, values float32 Opened J1741_class_02_00075_volume.mrc as #4, grid size 240,240,240, pixel 2.33, shown at level 0.0857, step 1, values float32 Opened J1741_class_03_00075_volume.mrc as #5, grid size 240,240,240, pixel 2.33, shown at level 0.0673, step 1, values float32 Opened J1741_class_04_00075_volume.mrc as #6, grid size 240,240,240, pixel 2.33, shown at level 0.0974, step 1, values float32 Opened J1741_class_05_00075_volume.mrc as #7, grid size 240,240,240, pixel 2.33, shown at level 0.0705, step 1, values float32 Opened J1741_class_06_00075_volume.mrc as #8, grid size 240,240,240, pixel 2.33, shown at level 0.0727, step 1, values float32 Opened J1741_class_07_00075_volume.mrc as #9, grid size 240,240,240, pixel 2.33, shown at level 0.13, step 1, values float32 Opened J1745_class_00_00094_volume.mrc as #10, grid size 192,192,192, pixel 2.91, shown at level 0.103, step 1, values float32 Opened J1745_class_01_00094_volume.mrc as #11, grid size 192,192,192, pixel 2.91, shown at level 0.0878, step 1, values float32 Opened J1745_class_02_00094_volume.mrc as #12, grid size 192,192,192, pixel 2.91, shown at level 0.0973, step 1, values float32 Opened J1745_class_03_00094_volume.mrc as #13, grid size 192,192,192, pixel 2.91, shown at level 0.107, step 1, values float32 Opened J1745_class_04_00094_volume.mrc as #14, grid size 192,192,192, pixel 2.91, shown at level 13.4, step 1, values float32 Opened J1745_class_05_00094_volume.mrc as #15, grid size 192,192,192, pixel 2.91, shown at level 5.97, step 1, values float32 Log from Thu Feb 27 15:22:49 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class001.mrc Opened Cl3D_j581_run_it025_class001.mrc as #1, grid size 294,294,294, pixel 1.9, shown at level 0.0158, step 2, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class002.mrc Opened Cl3D_j581_run_it025_class002.mrc as #2, grid size 294,294,294, pixel 1.9, shown at level 0.0166, step 2, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class003.mrc Opened Cl3D_j581_run_it025_class003.mrc as #3, grid size 294,294,294, pixel 1.9, shown at level 0.0157, step 2, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class004.mrc Opened Cl3D_j581_run_it025_class004.mrc as #4, grid size 294,294,294, pixel 1.9, shown at level 0.0131, step 2, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class005.mrc Opened Cl3D_j581_run_it025_class005.mrc as #5, grid size 294,294,294, pixel 1.9, shown at level 0.013, step 2, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class006.mrc Opened Cl3D_j581_run_it025_class006.mrc as #6, grid size 294,294,294, pixel 1.9, shown at level 0.0154, step 2, values float32 > open > /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class007.mrc Opened Cl3D_j581_run_it025_class007.mrc as #7, grid size 294,294,294, pixel 1.9, shown at level 0.018, step 2, values float32 > tile 7 models tiled > tile 7 Expected a models specifier or a keyword > volume all step 1 > set bgColor white > lighting soft > lighting simple > volume #1 level 0.01308 > volume #2 level 0.01493 > volume #2 level 0.0143 > volume #3 level 0.01453 > volume #4 level 0.01256 > volume #5 level 0.01323 > volume #6 level 0.01418 > save /Users/cvetkom/Desktop/image3.png supersample 3 > close #1-7 > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1528_010_volume_map.mrc Opened cryosparc_P17_J1528_010_volume_map.mrc as #1, grid size 588,588,588, pixel 0.95, shown at level 0.0454, step 4, values float32 > volume #1 step 1 > volume #1 level 0.0845 > volume #1 level 0.1119 > volume #1 level 0.09818 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_00_00075_volume.mrc Opened J1741_class_00_00075_volume.mrc as #2, grid size 240,240,240, pixel 2.33, shown at level 0.064, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_01_00075_volume.mrc Opened J1741_class_01_00075_volume.mrc as #3, grid size 240,240,240, pixel 2.33, shown at level 0.0741, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_02_00075_volume.mrc Opened J1741_class_02_00075_volume.mrc as #4, grid size 240,240,240, pixel 2.33, shown at level 0.0857, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_03_00075_volume.mrc Opened J1741_class_03_00075_volume.mrc as #5, grid size 240,240,240, pixel 2.33, shown at level 0.0673, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_04_00075_volume.mrc Opened J1741_class_04_00075_volume.mrc as #6, grid size 240,240,240, pixel 2.33, shown at level 0.0974, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_05_00075_volume.mrc Opened J1741_class_05_00075_volume.mrc as #7, grid size 240,240,240, pixel 2.33, shown at level 0.0705, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_06_00075_volume.mrc Opened J1741_class_06_00075_volume.mrc as #8, grid size 240,240,240, pixel 2.33, shown at level 0.0727, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_07_00075_volume.mrc Opened J1741_class_07_00075_volume.mrc as #9, grid size 240,240,240, pixel 2.33, shown at level 0.13, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_00_00094_volume.mrc Opened J1745_class_00_00094_volume.mrc as #10, grid size 192,192,192, pixel 2.91, shown at level 0.103, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_01_00094_volume.mrc Opened J1745_class_01_00094_volume.mrc as #11, grid size 192,192,192, pixel 2.91, shown at level 0.0878, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_02_00094_volume.mrc Opened J1745_class_02_00094_volume.mrc as #12, grid size 192,192,192, pixel 2.91, shown at level 0.0973, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_03_00094_volume.mrc Opened J1745_class_03_00094_volume.mrc as #13, grid size 192,192,192, pixel 2.91, shown at level 0.107, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_04_00094_volume.mrc Opened J1745_class_04_00094_volume.mrc as #14, grid size 192,192,192, pixel 2.91, shown at level 13.4, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_05_00094_volume.mrc Opened J1745_class_05_00094_volume.mrc as #15, grid size 192,192,192, pixel 2.91, shown at level 5.97, step 1, values float32 > volume all step 1 > hide #!15 models > hide #!14 models > hide #!13 models > hide #!12 models > hide #!11 models > hide #!10 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!5 models > hide #!6 models > hide #!4 models > hide #!3 models > show #!3 models > hide #!2 models > hide #!1 models > hide #!3 models > show #!2 models > volume #2 level 0.2493 > lighting soft > lighting simple > set bgColor black > set bgColor transparent > volume #2 level 0.2963 > volume #3 level 0.3843 > ui mousemode right zoom > volume #3 level 0.3973 > volume #3 level 0.3348 > show #!2 models > hide #!3 models > save /Users/cvetkom/Documents/chimera_sessions/20250227_ATPase_DNA_grip.cxs ——— End of log from Thu Feb 27 15:22:49 2025 ——— opened ChimeraX session > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > volume #4 level 0.387 > volume #4 level 0.3774 > volume #5 level 0.3801 > volume #5 level 0.2856 > volume #5 level 0.3318 > volume #5 level 0.3486 > volume #6 level 0.418 > lighting soft > lighting simple > volume #6 level 0.4659 > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!3 models > show #!3 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!3 models > hide #!6 models > show #!7 models > volume #7 level 0.3604 > volume #8 level 0.2682 > volume #8 level 0.2344 > volume #8 level 0.2947 > volume #9 level 0.6956 > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!5 models > volume #5 level 0.2877 > volume #5 level 0.3171 > volume #10 level 0.4639 > volume #10 level 0.4515 > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!10 models > show #!11 models > volume #11 level 0.4281 > volume #12 level 0.526 > volume #13 level 0.6189 > volume #13 level 0.6518 > volume #14 level 15.29 > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!6 models > show #!3 models > hide #!3 models > show #!3 models > hide #!6 models > show #!6 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > ui mousemode right zoom > save /Users/cvetkom/Documents/chimera_sessions/20250227_ATPase_DNA_grip.cxs ——— End of log from Thu Feb 27 16:32:14 2025 ——— opened ChimeraX session > hide #!6 models > show #!6 models > show #!2 models > hide #!6 models > show #!3 models > hide #!2 models > show #!6 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!6 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!7 models > hide #!7 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!3 models > hide #!3 models > show #!6 models > show #!3 models > hide #!6 models > show #!6 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!6 models > show #!4 models > hide #!4 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!11 models > hide #!11 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!13 models > show #!14 models > show #!15 models > hide #!15 models > hide #!14 models > hide #!13 models > show #!13 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > hide #!13 models > show #!10 models > show #!4 models > hide #!4 models > show #!4 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!4 models > show #!4 models > hide #!10 models > show #!10 models > hide #!10 models > show #!3 models > hide #!4 models > hide #!3 models > show #!3 models > show #!6 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!6 models > hide #!3 models > open > /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1549_007_volume_map.mrc Opened cryosparc_P17_J1549_007_volume_map.mrc as #16, grid size 588,588,588, pixel 0.95, shown at level 0.0482, step 4, values float32 > volume #16 step 1 > volume #16 level 0.1686 > volume #16 level 0.1246 > volume #16 level 0.1093 > volume #16 level 0.1055 > volume #16 level 0.1 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_00_00039_volume.mrc Opened J1757_class_00_00039_volume.mrc as #17, grid size 120,120,120, pixel 4.65, shown at level 0.123, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_01_00039_volume.mrc Opened J1757_class_01_00039_volume.mrc as #18, grid size 120,120,120, pixel 4.65, shown at level 0.116, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_02_00039_volume.mrc Opened J1757_class_02_00039_volume.mrc as #19, grid size 120,120,120, pixel 4.65, shown at level 0.113, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_03_00039_volume.mrc Opened J1757_class_03_00039_volume.mrc as #20, grid size 120,120,120, pixel 4.65, shown at level 0.108, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_04_00039_volume.mrc Opened J1757_class_04_00039_volume.mrc as #21, grid size 120,120,120, pixel 4.65, shown at level 0.105, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_05_00039_volume.mrc Opened J1757_class_05_00039_volume.mrc as #22, grid size 120,120,120, pixel 4.65, shown at level 0.112, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_06_00039_volume.mrc Opened J1757_class_06_00039_volume.mrc as #23, grid size 120,120,120, pixel 4.65, shown at level 0.107, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_07_00039_volume.mrc Opened J1757_class_07_00039_volume.mrc as #24, grid size 120,120,120, pixel 4.65, shown at level 0.113, step 1, values float32 > hide #!18 models > hide #!19 models > hide #!20 models > hide #!21 models > hide #!22 models > hide #!23 models > hide #!24 models > volume #17 level 0.1994 > volume #17 level 0.2377 > volume #18 level 0.2399 > volume #18 level 0.2839 > volume #18 level 0.2324 > volume #19 level 0.2826 > show #!17 models > hide #!17 models > volume #20 level 0.348 > volume #21 level 0.2206 > volume #22 level 0.3406 > volume #23 level 0.1761 > volume #24 level 0.3109 > show #!21 models > hide #!21 models > show #!20 models > hide #!20 models > hide #!24 models > show #!22 models > show #!23 models > hide #!22 models > show #!22 models > show #!24 models > hide #!23 models > show #!21 models > hide #!21 models > show #!21 models > hide #!21 models > show #!21 models > hide #!21 models > show #!21 models > hide #!21 models > show #!20 models > hide #!20 models > show #!19 models > show #!18 models > show #!20 models > show #!21 models > show #!17 models > hide #!22 models > show #!22 models > hide #!16 models > show #!16 models > hide #!17 models > show #!17 models > hide #!17 models > hide #!19 models > hide #!18 models > show #!18 models > hide #!18 models > hide #!21 models > hide #!20 models > hide #!24 models > open > /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_00_00061_volume.mrc Opened J1567_class_00_00061_volume.mrc as #25, grid size 120,120,120, pixel 4.65, shown at level 0.103, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_01_00061_volume.mrc Opened J1567_class_01_00061_volume.mrc as #26, grid size 120,120,120, pixel 4.65, shown at level 0.107, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_02_00061_volume.mrc Opened J1567_class_02_00061_volume.mrc as #27, grid size 120,120,120, pixel 4.65, shown at level 0.105, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_03_00061_volume.mrc Opened J1567_class_03_00061_volume.mrc as #28, grid size 120,120,120, pixel 4.65, shown at level 0.116, step 1, values float32 > open > /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_04_00061_volume.mrc Opened J1567_class_04_00061_volume.mrc as #29, grid size 120,120,120, pixel 4.65, shown at level 0.103, step 1, values float32 > hide #!22 models > hide #!26 models > hide #!27 models > hide #!28 models > hide #!29 models > volume #25 level 0.2732 > volume #25 level 0.3769 > show #!26 models > hide #!25 models > volume #26 level 0.2965 > show #!25 models > hide #!25 models > hide #!26 models > show #!27 models > volume #27 level 0.1864 > volume #28 level 0.3188 > volume #28 level 0.3298 > volume #29 level 0.319 > volume #29 level 0.3859 > volume #29 level 0.4027 > open /Users/cvetkom/Downloads/cryosparc_P17_J1757_volume_map_consensus.mrc Opened cryosparc_P17_J1757_volume_map_consensus.mrc as #30, grid size 120,120,120, pixel 4.65, shown at level 0.136, step 1, values float32 > hide #!29 models > hide #!16 models > show #!16 models > volume #30 level 0.1682 > show #!17 models > show #!18 models > show #!19 models > show #!20 models > show #!21 models > show #!22 models > show #!23 models > hide #!22 models > hide #!17 models > hide #!18 models > hide #!19 models > hide #!20 models > hide #!21 models > hide #!23 models > show #!23 models > hide #!23 models > show #!24 models > hide #!24 models > show #!24 models > show #!23 models > hide #!23 models > show #!22 models > show #!21 models > hide #!22 models > show #!22 models > hide #!21 models > show #!21 models > show #!20 models > show #!19 models > show #!18 models > show #!17 models > volume add #17,18,19,20,21,22 Opened volume sum as #31, grid size 120,120,120, pixel 4.65, shown at step 1, values float32 > hide #!24 models > volume #31 level 0.5557 > volume #31 level 0.5367 > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!18 models > hide #!18 models > show #!18 models > hide #!18 models > show #!19 models > hide #!19 models > show #!20 models > hide #!20 models > show #!21 models > hide #!21 models > show #!22 models > hide #!22 models > show #!23 models > hide #!23 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > volume add #17,18,19,20,21,22 Opened volume sum as #32, grid size 120,120,120, pixel 4.65, shown at step 1, values float32 > close #32 > close #31 > show #!24 models > hide #!24 models > show #!24 models > show #!23 models > hide #!23 models > show #!22 models > show #!21 models > hide #!21 models > show #!21 models > show #!20 models > show #!19 models > show #!18 models > show #!17 models > volume add #17,18,19,20,21,22,24 Opened volume sum as #31, grid size 120,120,120, pixel 4.65, shown at step 1, values float32 > volume #31 level 0.585 > volume #31 level 0.5 > show #!24 models > hide #!24 models > show #!24 models > hide #!24 models > show #!23 models > hide #!23 models > show #!24 models > show #!22 models > show #!21 models > show #!20 models > show #!19 models > show #!18 models > show #!17 models > hide #!24 models > show #!24 models > hide #!17 models > hide #!18 models > hide #!19 models > hide #!21 models > hide #!22 models > hide #!20 models > hide #!24 models > hide #!16 models > ui tool show ""Segment Map"" Segmenting volume sum, density threshold 0.500000 Showing 17 region surfaces 75 watershed regions, grouped to 17 regions Showing volume sum.seg - 17 regions, 17 surfaces > select #32.1 1 model selected Ungrouped to 2 regions > select #32.18 1 model selected Ungrouped to 2 regions > select #32.1 1 model selected Ungrouped to 2 regions > select #32.18 1 model selected Ungrouped to 2 regions > select #32.1 1 model selected Ungrouped to 2 regions > select #32.23 1 model selected Ungrouped to 2 regions > select #32.1 1 model selected Ungrouped to 2 regions > select #32.18 1 model selected Ungrouped to 2 regions > select #32.1 1 model selected Ungrouped to 2 regions > select #32.18 1 model selected Ungrouped to 2 regions > select #32.28 1 model selected Ungrouped to 2 regions > select #32.18 1 model selected Ungrouped to 0 regions > select #32.18 1 model selected Ungrouped to 0 regions > select #32.20 1 model selected Ungrouped to 2 regions > select #32.28 1 model selected Ungrouped to 2 regions > select #32.25 1 model selected Ungrouped to 2 regions > show #!17 models > show #!18 models > show #!19 models > hide #!19 models > hide #!18 models > hide #!17 models > show #!16 models > select #32.28 1 model selected Ungrouped to 2 regions > select #32.33 1 model selected Ungrouped to 0 regions > select #32.33 1 model selected Ungrouped to 0 regions > select #32.1 1 model selected > select add #32.27 2 models selected > select add #32.22 3 models selected > select add #32.21 4 models selected > select add #32.19 5 models selected > select add #32.25 6 models selected > select add #32.26 7 models selected Grouped 7 regions > select add #32.29 2 models selected > select add #32.18 3 models selected Grouped 3 regions > hide #!31 models > show #!29 models > hide #!29 models > show #!29 models > hide #!32 models > show #!32 models > hide #!29 models > show #!24 models > hide #!24 models > show #!24 models > hide #!32 models > show #!32 models > hide #!32 models > show #!32 models > hide #!32 models > show #!32 models > hide #!24 models > show #!23 models > hide #!23 models > show #!22 models > hide #!22 models > show #!21 models > hide #!21 models > show #!21 models > hide #!21 models > show #!20 models > hide #!20 models > show #!19 models > hide #!32 models > show #!32 models > hide #!19 models > show #!18 models > hide #!18 models > show #!17 models > hide #!17 models Showing 24 region surfaces > select #32.20 1 model selected Ungrouped to 2 regions > select #32.1 1 model selected > select add #32.19 2 models selected Grouped 2 regions Opened volume sum_imasked as #33, grid size 120,120,120, pixel 4.65, shown at step 1, values float32 > hide #!32 models > show #!32 models > hide #!32 models > show #!32 models > hide #!33 models > hide #!16 models > show #!24 models > show #!23 models > hide #!23 models > show #!22 models > show #!21 models > show #!20 models > show #!19 models > show #!18 models > show #!17 models > hide #!32 models > show #!32 models > hide #!32 models > show #!32 models > hide #!32 models > show #!32 models > hide #!24 models > hide #!22 models > hide #!21 models > hide #!20 models > hide #!19 models > hide #!18 models > hide #!17 models Showing 24 region surfaces > select #32.1 1 model selected Ungrouped to 2 regions > select #32.20 1 model selected Ungrouped to 3 regions > select #32.21 1 model selected Ungrouped to 0 regions > select #32.21 1 model selected Ungrouped to 0 regions > select #32.1 1 model selected Ungrouped to 7 regions > select #32.20 1 model selected > select #32.21 1 model selected Ungrouped to 0 regions > select #32.20 1 model selected Ungrouped to 2 regions > select #32.1 1 model selected Ungrouped to 2 regions > select #32.20 1 model selected Ungrouped to 2 regions > select #32.37 1 model selected Ungrouped to 0 regions > select #32.37 1 model selected Ungrouped to 0 regions > select #32.21 1 model selected Ungrouped to 0 regions > hide #!32 models > show #!33 models > ui mousemode right ""map eraser"" > volume erase #33 center 232.01,334.59,191.4 radius 158.31 > show #!16 models > ui tool show ""Map Filter"" > volume gaussian #33 sDev 1.21 Opened volume sum_imasked gaussian as #34, grid size 120,120,120, pixel 4.65, shown at step 1, values float32 > close #34 > volume gaussian #33 sDev 2 Opened volume sum_imasked gaussian as #34, grid size 120,120,120, pixel 4.65, shown at step 1, values float32 > close #33 > volume #34 level 0.5 > ui mousemode right zoom > save > /Users/cvetkom/Downloads/cryosparc_P17_J1757_volume_map_NCP_for_mask.mrc > models #34 > open /Users/cvetkom/Downloads/cryosparc_P17_J1765_mask.mrc Opened cryosparc_P17_J1765_mask.mrc as #33, grid size 120,120,120, pixel 4.65, shown at level 1, step 1, values float32 > volume #33 level 1 > volume #33 color #ffffb27d > volume #33 level 0.5139 > volume #33 level 1 > hide #!34 models > hide #!33 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!18 models > hide #!18 models > show #!19 models > hide #!19 models > show #!20 models > hide #!20 models > show #!21 models > hide #!21 models > show #!22 models > hide #!22 models > show #!23 models > hide #!23 models > show #!24 models > hide #!24 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1479/run_it025_class001.mrc Opened run_it025_class001.mrc as #35, grid size 520,520,520, pixel 0.95, shown at level 0.000296, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1479/run_it025_class002.mrc Opened run_it025_class002.mrc as #36, grid size 520,520,520, pixel 0.95, shown at level 0.000188, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1479/run_it025_class003.mrc Opened run_it025_class003.mrc as #37, grid size 520,520,520, pixel 0.95, shown at level 0.000293, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1479/run_it025_class004.mrc Opened run_it025_class004.mrc as #38, grid size 520,520,520, pixel 0.95, shown at level 0.000144, step 4, values float32 > hide #!16 models > hide #!23 models > volume all step 1 > volume #35 level 0.00175 > volume #35 level 0.001985 > volume #36 level 0.001419 > volume #36 level 0.002258 > volume #35 level 0.002231 > volume #37 level 0.001461 > volume #37 level 0.002052 > volume #38 level 0.003347 > volume #38 level 0.003643 > volume #38 level 0.003021 > volume #38 level 0.002881 > volume #38 level 0.003099 > volume #37 level 0.002479 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class001.mrc Opened run_it025_class001.mrc as #39, grid size 520,520,520, pixel 0.95, shown at level 0.000136, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class002.mrc Opened run_it025_class002.mrc as #40, grid size 520,520,520, pixel 0.95, shown at level 0.000382, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class003.mrc Opened run_it025_class003.mrc as #41, grid size 520,520,520, pixel 0.95, shown at level 0.000168, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class004.mrc Opened run_it025_class004.mrc as #42, grid size 520,520,520, pixel 0.95, shown at level 0.000171, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class005.mrc Opened run_it025_class005.mrc as #43, grid size 520,520,520, pixel 0.95, shown at level 0.000178, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class006.mrc Opened run_it025_class006.mrc as #44, grid size 520,520,520, pixel 0.95, shown at level 0.000256, step 4, values float32 > volume all step 1 > volume #39 level 0.003951 > volume #40 level 0.002104 > volume #41 level 0.000915 > volume #41 level 0.002577 > volume #42 level 0.002549 > volume #42 level 0.00269 > volume #43 level 0.001448 > volume #43 level 0.002702 > volume #44 level 0.002278 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class001.mrc Opened run_it025_class001.mrc as #45, grid size 520,520,520, pixel 0.95, shown at level 0.00022, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class002.mrc Opened run_it025_class002.mrc as #46, grid size 520,520,520, pixel 0.95, shown at level 0.000144, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class003.mrc Opened run_it025_class003.mrc as #47, grid size 520,520,520, pixel 0.95, shown at level 0.000205, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class004.mrc Opened run_it025_class004.mrc as #48, grid size 520,520,520, pixel 0.95, shown at level 0.00024, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class005.mrc Opened run_it025_class005.mrc as #49, grid size 520,520,520, pixel 0.95, shown at level 0.000309, step 4, values float32 > volume all step 1 > volume #45 level 0.002525 > volume #45 level 0.002927 > volume #46 level 0.002752 > volume #47 level 0.002429 > volume #48 level 0.002541 > volume #49 level 0.002957 > show #!49 models > hide #!49 models > show #!48 models > hide #!48 models > show #!47 models > hide #!47 models > show #!49 models > hide #!49 models > volume #46 level 0.002752 > hide #!36 models > show #!36 models > show #!38 models > hide #!36 models > hide #!38 models > show #!36 models > hide #!36 models > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1476/run_it025_class002.mrc Opened run_it025_class002.mrc as #50, grid size 520,520,520, pixel 0.95, shown at level 0.000201, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1476/run_it025_class006.mrc Opened run_it025_class006.mrc as #51, grid size 520,520,520, pixel 0.95, shown at level 0.000132, step 4, values float32 > volume all step 1 > volume #50 level 0.002655 > volume #50 level 0.002444 > volume #51 level 0.002852 > volume #50 level 0.001989 > volume #51 level 0.002679 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1475/run_it025_class001.mrc Opened run_it025_class001.mrc as #52, grid size 520,520,520, pixel 0.95, shown at level 0.000198, step 4, values float32 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1475/run_it025_class004.mrc Opened run_it025_class004.mrc as #53, grid size 520,520,520, pixel 0.95, shown at level 0.00011, step 4, values float32 > volume all step 1 > volume #52 level 0.00258 > volume #52 level 0.002524 > volume #53 level 0.002425 > volume #52 level 0.002093 > volume #53 level 0.002078 > open /Volumes/lab- > costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1474/run_it025_class002.mrc Opened run_it025_class002.mrc as #54, grid size 520,520,520, pixel 0.95, shown at level 0.00018, step 4, values float32 > volume all step 1 > volume #54 level 0.002427 > volume #54 level 0.001525 > open /Users/cvetkom/Downloads/cryosparc_P17_J1626_009_volume_map.mrc Opened cryosparc_P17_J1626_009_volume_map.mrc as #55, grid size 588,588,588, pixel 0.95, shown at level 0.0688, step 4, values float32 > volume #55 step 1 > lighting soft > volume #55 level 0.07079 > volume #55 level 0.09629 > volume #55 level 0.07181 > hide #!55 models > show #!36 models > lighting simple [Repeated 1 time(s)] > show #!42 models > hide #!36 models > show #!36 models > hide #!36 models > show #!36 models > hide #!36 models > hide #!42 models > open /Users/cvetkom/Downloads/cryosparc_P17_J1598_volume_map.mrc Opened cryosparc_P17_J1598_volume_map.mrc as #56, grid size 520,520,520, pixel 0.95, shown at level 0.00289, step 4, values float32 > open /Users/cvetkom/Downloads/cryosparc_P17_J1600_mask.mrc Opened cryosparc_P17_J1600_mask.mrc as #57, grid size 520,520,520, pixel 0.95, shown at level 0.799, step 4, values float32 > hide #!56 models > show #!56 models > volume #56 level 0.03581 > volume #56 step 1 > volume #57 color #ffb2ff82 > volume #57 step 1 > open /Users/cvetkom/Downloads/cryosparc_P17_J1762_008_volume_map.mrc Opened cryosparc_P17_J1762_008_volume_map.mrc as #58, grid size 588,588,588, pixel 0.95, shown at level 0.061, step 4, values float32 > volume #58 step 1 > volume #58 level 0.09631 > volume #58 level 0.07799 > lighting soft > open /Users/cvetkom/Downloads/cryosparc_P17_J1759_008_volume_map.mrc Opened cryosparc_P17_J1759_008_volume_map.mrc as #59, grid size 588,588,588, pixel 0.95, shown at level 0.0499, step 4, values float32 > hide #!58 models > volume #59 step 1 > volume #59 level 0.1244 > lighting simple > volume #59 level 0.1026 > ui tool show ""Side View"" > volume #59 level 0.1135 > lighting soft > lighting full > lighting simple > open /Users/cvetkom/Downloads/cryosparc_P17_J1760_007_volume_map.mrc Opened cryosparc_P17_J1760_007_volume_map.mrc as #60, grid size 588,588,588, pixel 0.95, shown at level 0.047, step 4, values float32 > open /Users/cvetkom/Downloads/cryosparc_P17_J1761_008_volume_map.mrc Opened cryosparc_P17_J1761_008_volume_map.mrc as #61, grid size 588,588,588, pixel 0.95, shown at level 0.0467, step 4, values float32 > volume #60 step 1 > volume #61 step 1 > volume #60 level 0.1558 > volume #60 level 0.1281 > volume #61 level 0.1442 > open /Users/cvetkom/Downloads/cryosparc_P17_J1748_008_volume_map.mrc Opened cryosparc_P17_J1748_008_volume_map.mrc as #62, grid size 588,588,588, pixel 0.95, shown at level 0.0485, step 4, values float32 > open /Users/cvetkom/Downloads/cryosparc_P17_J1749_007_volume_map.mrc Opened cryosparc_P17_J1749_007_volume_map.mrc as #63, grid size 588,588,588, pixel 0.95, shown at level 0.048, step 4, values float32 > volume #62 step 2 > volume #62 step 1 > volume #63 step 1 > volume #62 level 0.1539 > volume #63 level 0.1446 > volume #62 color darkgrey [Repeated 1 time(s)] > volume #62 color #929292 > volume #62 color darkgrey > volume #62 color #929292 > volume #60 level 0.13 > volume #62 level 0.13 > volume #62 level 0.135 > volume #62 level 0.14 > volume #61 level 0.14 > volume #63 level 0.14 > show #!59 models > hide #!62 models > volume #59 color #009193 > volume #59 level 0.13 > volume #59 level 0.12 > lighting soft [Repeated 1 time(s)] > lighting simple > hide #!59 models > show #!62 models > show #!63 models > hide #!62 models > show #!62 models > hide #!63 models > hide #!62 models > show #!59 models > show #!62 models > hide #!62 models > show #!63 models > hide #!59 models > show #!59 models > hide #!63 models > show #!63 models > hide #!63 models > hide #!59 models > show #!60 models > show #!62 models > hide #!62 models > show #!61 models > hide #!61 models > show #!61 models > hide #!60 models > show #!60 models > hide #!61 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!60 models > show #!60 models > hide #!60 models > hide #!62 models > show #!61 models > show #!63 models > hide #!63 models > show #!63 models > hide #!63 models > show #!63 models > hide #!63 models > show #!63 models > hide #!63 models > show #!63 models > hide #!63 models > hide #!61 models > show #!62 models > volume #63 level 0.1 > volume #63 level 0.06 > volume #63 level 0.08 > volume #63 level 0.085 > volume #63 level 0.09 > volume #62 level 0.09 > show #!63 models > hide #!62 models > show #!62 models > hide #!63 models > show #!63 models > hide #!63 models > show #!63 models > hide #!63 models > show #!63 models > hide #!63 models > hide #!62 models > show #!62 models > show #!63 models > save /Users/cvetkom/Documents/chimera_sessions/20250228_post_polish_mix.cxs ——— End of log from Fri Feb 28 11:55:25 2025 ——— opened ChimeraX session Showing volume sum.seg - 36 regions, 36 surfaces OpenGL version: 4.1 ATI-6.1.13 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2069.80.3.0.0 (iBridge: 22.16.13051.0.0,0) OS Loader Version: 582~3311 Software: System Software Overview: System Version: macOS 15.3.1 (24D70) Kernel Version: Darwin 24.3.0 Time since boot: 6 days, 8 hours, 28 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2415: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 7MT016923MAL Mirror: Off Online: Yes Rotation: Supported Adapter Type: DVI or HDMI Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 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 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: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 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: 1.18.1 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 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: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX