id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19902 Crash on Mac waking from sleep zrizvi@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.6.1-arm64-arm-64bit ChimeraX Version: 1.10.dev202503130118 (2025-03-13 01:18:56 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. 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Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"" Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at level 14, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size 443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32 Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size 443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32 Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32 Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443, pixel 0.5, shown at level 5.07, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy as #16, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size 443,443,443, pixel 0.5, shown at level 6.22, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size 443,443,443, pixel 0.5, shown at level 2.89, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size 443,443,443, pixel 0.5, shown at level 2.84, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size 443,443,443, pixel 0.5, shown at level 2.85, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size 443,443,443, pixel 0.5, shown at level 2.11, step 1, values float32 Opened 10. int1 vvd+imid NU J2527_map_emready2.mrc as #18, grid size 443,443,443, pixel 0.5, shown at level 0.9, step 1, values float32 Opened 11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc as #19, grid size 443,443,443, pixel 0.5, shown at level 1.16, step 1, values float32 Opened 12. combination of 10 and 11 as #20, grid size 443,443,443, pixel 0.5, shown at level 0.862, step 1, values float32 Log from Tue Feb 24 16:13:45 2026UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/ChimeraX/fig 2.cxs"" Opened cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at level 14, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Log from Thu Jul 24 11:26:36 2025UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making/fig 2.cxs"" Opened cryosparc_P341_J1537_local refine on 1464.mrc as #1, grid size 300,300,300, pixel 0.833, shown at level 0.227, step 1, values float32 Opened cryosparc_P341_J1554_local refine on 1550.mrc as #2, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1575_map_sharp.mrc deepEM as #3, grid size 300,300,300, pixel 0.833, shown at level 0.253, step 1, values float32 Opened cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1642_local refine.mrc as #5, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1464_NU refine.mrc as #6, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened cryosparc_P341_J1473_localrefine.mrc as #7, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1550_Nurefine.mrc as #8, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at level 14, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Log from Thu Jul 24 01:33:11 2025UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /fig 2.cxs"" Opened cryosparc_P341_J1537_local refine on 1464.mrc as #1, grid size 300,300,300, pixel 0.833, shown at level 0.227, step 1, values float32 Opened cryosparc_P341_J1554_local refine on 1550.mrc as #2, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1575_map_sharp.mrc deepEM as #3, grid size 300,300,300, pixel 0.833, shown at level 0.253, step 1, values float32 Opened cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1642_local refine.mrc as #5, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1464_NU refine.mrc as #6, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened cryosparc_P341_J1473_localrefine.mrc as #7, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1550_Nurefine.mrc as #8, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Log from Thu Jul 24 00:56:27 2025UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/figure for > Gabe modified/vvd figure making.cxs"" Opened cryosparc_P341_J1537_local refine on 1464.mrc as #1, grid size 300,300,300, pixel 0.833, shown at level 0.227, step 1, values float32 Opened cryosparc_P341_J1554_local refine on 1550.mrc as #2, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1575_map_sharp.mrc deepEM as #3, grid size 300,300,300, pixel 0.833, shown at level 0.253, step 1, values float32 Opened cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1642_local refine.mrc as #5, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1464_NU refine.mrc as #6, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened cryosparc_P341_J1473_localrefine.mrc as #7, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1550_Nurefine.mrc as #8, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Log from Tue Apr 29 15:52:59 2025UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Desktop/vvd figure making.cxs"" Opened cryosparc_P341_J1537_local refine on 1464.mrc as #1, grid size 300,300,300, pixel 0.833, shown at level 0.227, step 1, values float32 Opened cryosparc_P341_J1554_local refine on 1550.mrc as #2, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1575_map_sharp.mrc deepEM as #3, grid size 300,300,300, pixel 0.833, shown at level 0.253, step 1, values float32 Opened cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1642_local refine.mrc as #5, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1464_NU refine.mrc as #6, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened cryosparc_P341_J1473_localrefine.mrc as #7, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1550_Nurefine.mrc as #8, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Log from Tue Apr 29 13:11:33 2025UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/zrizvi/Downloads/cryosparc_P341_J1537_004_volume_map.mrc Opened cryosparc_P341_J1537_004_volume_map.mrc as #1, grid size 300,300,300, pixel 0.833, shown at level 0.0281, step 2, values float32 > open /Users/zrizvi/Downloads/cryosparc_P341_J1554_005_volume_map.mrc Opened cryosparc_P341_J1554_005_volume_map.mrc as #2, grid size 300,300,300, pixel 0.833, shown at level 0.0434, step 2, values float32 > open /Users/zrizvi/Downloads/cryosparc_P341_J1575_map_sharp.mrc Opened cryosparc_P341_J1575_map_sharp.mrc as #3, grid size 300,300,300, pixel 0.833, shown at level 0.00032, step 2, values float32 > open /Users/zrizvi/Downloads/cryosparc_P341_J1614_005_volume_map.mrc Opened cryosparc_P341_J1614_005_volume_map.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.0429, step 2, values float32 > open /Users/zrizvi/Downloads/cryosparc_P341_J1642_005_volume_map.mrc Opened cryosparc_P341_J1642_005_volume_map.mrc as #5, grid size 300,300,300, pixel 0.833, shown at level 0.0424, step 2, values float32 > open ""/Users/zrizvi/Downloads/cryosparc_P341_J1464_008_volume_map (1).mrc"" Opened cryosparc_P341_J1464_008_volume_map (1).mrc as #6, grid size 300,300,300, pixel 0.833, shown at level 0.0314, step 2, values float32 > open ""/Users/zrizvi/Downloads/cryosparc_P341_J1473_004_volume_map (1).mrc"" Opened cryosparc_P341_J1473_004_volume_map (1).mrc as #7, grid size 300,300,300, pixel 0.833, shown at level 0.0324, step 2, values float32 > volume #1 step 1 > volume #2 step 1 > volume #3 step 1 > volume #4 step 1 > volume #5 step 1 > volume #6 step 1 > volume #7 step 1 > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > volume #1 level 0.201 > show #!2 models > volume #2 level 0.2044 > show #!6 models > volume #6 level 0.1538 > rename #2 ""cryosparc_P341_J1554_0local refine on 1464.mrc"" > rename #2 ""cryosparc_P341_J1554_local refine on 1464.mrc"" > rename #1 ""cryosparc_P341_J1537_local refine on 1464.mrc"" > rename #2 ""cryosparc_P341_J1554_local refine on 1550.mrc"" > open ""/Users/zrizvi/Downloads/cryosparc_P341_J1550_006_volume_map (2).mrc"" Opened cryosparc_P341_J1550_006_volume_map (2).mrc as #8, grid size 300,300,300, pixel 0.833, shown at level 0.0282, step 2, values float32 > volume #8 step 1 > volume #8 level 0.1757 > hide #!8 models > hide #!2 models > hide #!6 models > show #!6 models > hide #!1 models > show #!1 models > hide #!6 models > show #!6 models > hide #!1 models > show #!1 models > hide #!6 models > open /Users/zrizvi/Downloads/cryosparc_P341_J1735_007_volume_map.mrc Opened cryosparc_P341_J1735_007_volume_map.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.0299, step 2, values float32 > volume #9 step 1 > volume #9 level 0.1746 > tile 2 models tiled > show #!2 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > show #!8 models > tile 9 models tiled > hide #!3 models > show #!3 models > volume #3 level 0.2531 > volume #4 level 0.2407 > volume #5 level 0.2597 > volume #6 level 0.2049 > volume #6 level 0.1582 > volume #7 level 0.1171 > volume #7 level 0.2217 > volume #8 level 0.2374 > volume #9 level 0.2058 > rename #3 ""cryosparc_P341_J1575_map_sharp.mrc deepEM"" > rename #4 cryosparc_P341_J1614_localrefine.mrc > rename #5 ""cryosparc_P341_J1642_local refine.mrc"" > rename #6 ""cryosparc_P341_J1464_NU refine.mrc"" > rename #7 cryosparc_P341_J1473_localrefine.mrc > rename #8 cryosparc_P341_J1550_Nurefine).mrc > rename #8 cryosparc_P341_J1550_Nurefine.mrc > rename #9 cryosparc_P341_J1735_NUrefine.mrc > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!7 models > ~tile > hide #!6 models > hide #!8 models > hide #!9 models > show #!6 models > hide #!6 models > show #!8 models > volume #8 level 0.158 > hide #!8 models > show #!9 models > volume #9 level 0.158 > show #!7 models > show #!6 models > hide #!7 models > show #!8 models > tile 3 models tiled > hide #!6 models > ~tile > tile 2 models tiled > ~tile > color #9 #99bfe56a models > color #9 #99bfe56d models > hide #!8 models > color #9 #99bfe5ff models > show #!1 models > show #!2 models > show #!4 models > show #!5 models > show #!7 models > ~tile > hide #!9 models > tile 5 models tiled > volume #1 level 0.2267 > hide #!1 models > volume #2 level 0.3042 > volume #4 level 0.304 > volume #5 level 0.304 > volume #7 level 0.304 > hide #!7 models > ~tile > tile 3 models tiled > hide #!5 models > hide #!2 models > show #!9 models > ~tile > rename #9 ""cryosparc_P341_J1735_NUrefine selected.mrc"" > rename #4 ""cryosparc_P341_J1614_localrefine. selected.mrc"" > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/2. processing > in coot/vvd.pdb"" > hide #!9 models > hide #!4 models > close #10 > show #!4 models > show #!9 models > save ""/Users/zrizvi/Desktop/vvd figure making.cxs"" includeMaps true ——— End of log from Tue Apr 29 13:11:33 2025 ——— > view name session-start opened ChimeraX session > hide #!4 models > hide #!9 models > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/ACB manuscript > shared folder/4. Results extended/Figure 5/model building/2. With > ikaros/with deg47 only/CombineFocusedMaps_71/composite_map.ccp4"" Opened composite_map.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at level 0.744, step 2, values float32 > volume #10 step 1 > volume #10 level 10.76 > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/2. processing > in coot/8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb"" Chain information for 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb #11 --- Chain | Description A | No description available B | No description available > hide #!10 models > select #11/A 6318 atoms, 6434 bonds, 824 residues, 1 model selected > color sel light gray > select clear > color #11/A:1-710 light blue > color #11/A:710-5000 steel blue > color #11/A:392-709 cornflower blue > color #11/B:1-190 navajowhite > color #11/B:191-320 light salmon > color #11/B:321-500 tomato > show #!10 models > volume #10 level 9.956 > select ::name=""101"" 28 atoms, 30 bonds, 1 residue, 1 model selected > color sel lime > select clear > color zone #10 near #11 distance 5 > color zone #11 near #10 distance 8 color zone: No surfaces specified. > color zone #10 near #11 distance 8 > hide #!11 models > graphics silhouettes true > lighting shadows true > lighting soft > set bgColor white > show #!11 models > hide #!11 models > rename #10 ""composite_map on EMReady2 maps of 1735 and 1614.ccp4"" > save ""/Users/zrizvi/Desktop/vvd figure making.cxs"" includeMaps true ——— End of log from Tue Apr 29 15:52:59 2025 ——— > view name session-start opened ChimeraX session > show #!11 models > hide #!10 models > show #!10 models > color #10 #b2b2b2da models > color #10 #b2b2b2ff models > color zone #10 near #11 distance 8 > color zone #10 near #11 distance 10 > hide #!11 models > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/figure for > Gabe modified/vvd.pdb"" > hide #!10 models > show #!10 models > close #12 > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/figure for > Gabe modified/final.pdb"" Chain information for final.pdb #12 --- Chain | Description B | No description available C | No description available > mmaker #12 to #11 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb, chain A (#11) with final.pdb, chain B (#12), sequence alignment score = 3652.5 RMSD between 786 pruned atom pairs is 0.524 angstroms; (across all 824 pairs: 0.911) > hide #!10 models > show #!11 models > hide #!11 models > hide #!12 models > show #!11 models > color #!11 byhetero > select clear > show #!12 models > hide #!12 models > show #!12 models > close #12 > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/figure for > Gabe modified/7u8ffinallylinkedtoVVD.pdb"" Chain information for 7u8ffinallylinkedtoVVD.pdb #12 --- Chain | Description B | No description available C | No description available > close #12 > show #!10 models > hide #!11 models > camera ortho > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /Figure 2a.png"" width 1800 height 1532 supersample 4 > transparentBackground true > show #!11 models > color #10 #b2b2b2c0 models > color #10 #b2b2b2bf models > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 11/B > select /B:264 14 atoms, 15 bonds, 1 residue, 1 model selected > select /B:264 14 atoms, 15 bonds, 1 residue, 1 model selected > select clear > ui tool show ""Side View"" > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /Figure 2b.png"" width 1800 height 1532 supersample 4 > transparentBackground true > open 8cvp 8cvp title: Cereblon-DDB1 in the Apo form [more info...] Chain information for 8cvp #12 --- Chain | Description | UniProt A | DNA damage-binding protein 1 | DDB1_HUMAN 1-1140 B | Protein cereblon | CRBN_HUMAN 1-442 Non-standard residues in 8cvp #12 --- ZN — zinc ion > mmaker #12 to #11 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb, chain A (#11) with 8cvp, chain A (#12), sequence alignment score = 5335.5 RMSD between 824 pruned atom pairs is 0.011 angstroms; (across all 824 pairs: 0.011) > hide #!10 models > ui tool show ""Show Sequence Viewer"" > sequence chain #12/B Alignment identifier is 12/B > select #12/B:264 14 atoms, 15 bonds, 1 residue, 1 model selected > select #12/B:264 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > color #12 darkgrey > select clear > show #!10 models > hide #!11 models > show #!11 models > select add #12 10112 atoms, 10284 bonds, 6 pseudobonds, 1485 residues, 4 models selected > color (#!12 & sel) cornflower blue > select clear > color #12/A:1-710 light blue > color #12/A:710-5000 steel blue > color #12/A:392-709 cornflower blue > color #12/B:1-190 navajowhite > color #12/B:191-320 light salmon > color #12/B:321-500 tomato > hide #!11 models > show #!11 models > hide #!12 models > color #10 #b2b2b2ff models > ui tool show ""Surface Color"" > ui tool show ""Surface Zone"" > ui tool show ""Volume Viewer"" > ui tool show ""Color Zone"" > color zone #10 near #11 distance 3.83 > color single #10 > hide #!11 atoms > color zone #10 near #11 distance 3.83 > color single #10 > color #10 #b2b2b2d2 models > color #10 #b2b2b2d1 models > select ::name=""101"" 28 atoms, 30 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select ::name=""101"" 28 atoms, 30 bonds, 1 residue, 1 model selected > color sel lime > select clear > hide #!10 models > select #11/B:264 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select clear > show #!10 models > ui tool show ""Volume Viewer"" > ui tool show ""Surface Zone"" > ui tool show ""Surface Color"" > ui tool show ""Color Zone"" Need to color zone map before it can be split [Repeated 1 time(s)] > color zone #10 near #11 distance 5 > volume splitbyzone #10 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 > select add #13.12 2 models selected > hide #!13.11 models > hide #!13.10 models > hide #!13.9 models > hide #!13.8 models > hide #!13.7 models > hide #!13.6 models > hide #!13.5 models > hide #!13.4 models > hide #!13.3 models > hide #!13.2 models > hide #!13.1 models > show #!10 models > color single #10 > hide #!13 models > show #!13 models > hide #!13 models > select add #13 25 models selected > select subtract #13 Nothing selected > hide #!10 models > show #!13 models > show #!10 models > hide #!10 models > color #13.2 darkgrey models > color #13.3 darkgrey models > color #13.4 darkgrey models > color #13.5 darkgrey models > color #13.6 darkgrey models > color #13.7 darkgrey models > color #13.8 darkgrey models > color #13.9 darkgrey models > color #13.10 darkgrey models > color #13.11 darkgrey models > show #!13.1 models > show #!13.2 models > show #!13.3 models > show #!13.4 models > show #!13.5 models > show #!13.6 models > show #!13.7 models > show #!13.8 models > show #!13.9 models > show #!13.10 models > show #!13.11 models > select add #13 25 models selected > select subtract #13.12 23 models selected > combine sel No structures specified > show #!10 models > hide #!10 models > show #!10 models > hide #!13.1 models > select subtract #13.1 21 models selected > select subtract #13.3 19 models selected > select add #13 25 models selected > select subtract #13 Nothing selected > hide #!13.2 models > hide #!13.3 models > hide #!13.4 models > hide #!13.5 models > hide #!13.6 models > hide #!13.7 models > hide #!10 models > show #!13.1 models > show #!13.3 models > hide #!13.3 models > show #!13.2 models > show #!13.3 models > show #!13.4 models > show #!13.5 models > show #!13.6 models > show #!13.7 models > hide #!11 models > show #!12 models > hide #!13 models > color #!12 byhetero > hide #!12.2 models Cell requested for row 12 is out of bounds for table with 27 rows! Resizing table model. > show #!13 models > hide #!13.2 models > hide #!13.1 models > hide #!13.3 models > hide #!13.4 models > hide #!13.5 models > hide #!13.6 models > hide #!13.7 models > hide #!13.9 models > hide #!13.8 models > hide #!13.10 models > hide #!13.11 models > show #!10 models > color #10 #b2b2b277 models > color #10 #b2b2b278 models > hide #!13.12 models > show #!13.12 models > ui tool show ""Side View"" > color #13.12 #00ff00db models > color #13.12 #00ff00b1 models > color #13.12 #00ff00b0 models > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > graphics silhouettes false > graphics silhouettes true > lighting soft > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /Figure 2c.png"" width 1800 height 1619 supersample 4 > transparentBackground true > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /fig 2.cxs"" includeMaps true ——— End of log from Thu Jul 24 00:56:27 2025 ——— > view name session-start opened ChimeraX session > show #!11 models > hide #!12 models > hide #!13 models > color #!11 byhetero > select clear > color #10 #b2b2b2b3 models > ui tool show ""Side View"" > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /Figure 2b.png"" width 1800 height 1532 supersample 4 > transparentBackground true > show #!13 models > hide #!11 models > show #!12 models > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /Figure 2c.png"" width 1800 height 1532 supersample 4 > transparentBackground true > show #!11 models > hide #!12 models > hide #!13 models > hide #!10 models > select #11/B:287 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select clear > show #!10 models > hide #!10 models > select #11/B:318 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select clear > show #!10 models > color #10 #d6d6d6ff models > color #10 #d6d6d6b3 models > select clear > volume #10 level 12 > volume #10 level 14.05 > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /Figure 2b.png"" width 1800 height 1532 supersample 4 > transparentBackground true > show #!13 models > hide #!11 models > show #!12 models > color #13 #d6d6d6ff models > color #13 #d6d6d6b3 models > hide #!10 models > select add #13 25 models selected > color #13.12.1 lime > select clear > show #!10 models > ui tool show ""Side View"" > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /Figure 2c.png"" width 1800 height 1471 supersample 4 > transparentBackground true > hide #!13 models > hide #!10 models > hide #!12 models > show #!11 models Drag select of 43 atoms, 49 residues, 45 bonds > show sel atoms > select clear > ui mousemode right distance > distance #11/B:502@F27 #11/B:261@CD2 Distance between 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb #11/B 101 502 F27 and LEU 261 CD2: 3.388Å > distance #11/B:502@C25 #11/B:260@NE2 Distance between 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb #11/B 101 502 C25 and GLN 260 NE2: 1.665Å > distance #11/B:502@C20 #11/B:318@SG Distance between 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb #11/B 101 502 C20 and CYS 318 SG: 3.698Å Cell requested for row 0 is out of bounds for table with 15 rows! Resizing table model. > morph #12 to #11 Expected a keyword > volume morph #12 to #11 Expected a keyword > vop morph #12 to #11 > volume morph #12 to #11 Expected a keyword > vop morph #12 #11 volume morph requires 2 or more volumes, got 0 > morph #12 #11 Computed 51 frame morph #15 > coordset #15 1,51 > hide #!15 models > show #!12 models Drag select of 11 atoms, 70 residues, 12 bonds > show sel atoms > select clear > show #!11 models > hide #!12 models > show #!12 models > close #15 > morph #12 #11 Computed 51 frame morph #15 > coordset #15 1,51 > morph #12 #11 Computed 51 frame morph #16 > coordset #16 1,51 > morph #12 #11 Computed 51 frame morph #17 > coordset #17 1,51 > close #15 > close #16 > close #17 > show #!11 models > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /fig 2.cxs"" includeMaps true ——— End of log from Thu Jul 24 01:33:11 2025 ——— > view name session-start opened ChimeraX session > close #1 > close #2 > close #3 > close #5 > close #6 > close #7 > close #8 > show #!10 models > show #!13 models > hide #!13 models > hide #!10 models > show #!12 models > hide #!14 models > color #12 #d6d6d6ff > color #12 silver > mmaker #12 to #11 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb, chain A (#11) with 8cvp, chain A (#12), sequence alignment score = 5335.5 RMSD between 824 pruned atom pairs is 0.011 angstroms; (across all 824 pairs: 0.011) > hide atoms > select ::name=""101"" 28 atoms, 30 bonds, 1 residue, 1 model selected > show sel atoms > select #11/B:264 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select #12/B:264 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select clear > color byhetero > select clear > ui tool show ""Side View"" > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/ChimeraX/fig 2.cxs"" includeMaps true > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making/fig2a zoom2.png"" width 1800 height 1532 supersample 4 > transparentBackground true > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/ChimeraX/fig 2.cxs"" includeMaps true ——— End of log from Thu Jul 24 11:26:36 2025 ——— > view name session-start opened ChimeraX session > hide #!11 models > show #!11 models > show #!4 models > show #!9 models > view > show #!10 models > hide #!9 models > hide #!4 models > hide #!12 models > show #!13 models > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/open/J2526_map_emready2.mrc"" Opened J2526_map_emready2.mrc as #1, grid size 443,443,443, pixel 0.5, shown at level 1.01, step 2, values float32 > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig > maps/open/J2540_005_volume_map_emready2.mrc"" Opened J2540_005_volume_map_emready2.mrc as #2, grid size 443,443,443, pixel 0.5, shown at level 1.2, step 2, values float32 > vop max #1 #2 Opened volume maximum as #3, grid size 443,443,443, pixel 0.5, shown at step 1, values float32 > rename #3 ""combination of 2526 and 2540 emready2"" > rename #1 ""open- vvd+imid J2526_map_emready2.mrc"" > rename #1 ""open- vvd+imid NU J2526_map_emready2.mrc"" > rename #2 ""open- vvd+imid local J2540_005_volume_map_emready2.mrc"" > hide #!11 models > hide #!13 models > show #!13 models > hide #!13 models > select add #3 2 models selected > graphics silhouettes false > lighting shadows true intensity 0.5 > lighting soft > lighting full > volume #1 step 1 > volume #2 step 1 > volume #3 level 3.516 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.97508,-0.17567,0.13548,12.133,0.1943,0.38153,-0.9037,165.36,0.10706,0.90751,0.40616,-72.098 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.97508,-0.17567,0.13548,26.737,0.1943,0.38153,-0.9037,162.12,0.10706,0.90751,0.40616,-74.124 > volume #3 level 5.573 > fitmap #3 inMap #10 Fit map combination of 2526 and 2540 emready2 in map composite_map on EMReady2 maps of 1735 and 1614.ccp4 using 340198 points correlation = 0.9503, correlation about mean = 0.6492, overlap = 5.013e+07 steps = 168, shift = 14.6, angle = 12.4 degrees Position of combination of 2526 and 2540 emready2 (#3) relative to composite_map on EMReady2 maps of 1735 and 1614.ccp4 (#10) coordinates: Matrix rotation and translation 0.96196967 -0.27233362 0.02118389 54.69880809 0.09346611 0.25529558 -0.96233479 187.78850372 0.25666796 0.92771686 0.27104057 -69.01712395 Axis 0.97451791 -0.12141649 0.18860775 Axis point 0.00000000 144.90433503 85.21030045 Rotation angle (degrees) 75.86822137 Shift along axis 17.48718173 > select clear > ui mousemode right translate > volume #3 level 2.711 > show #!11 models > hide #!10 models > color #3 #b2ffffa9 models > select clear > color zone #3 near #11 distance 8 > select clear > hide #!11 atoms > color zone #3 near #11 distance 8 > color #!11 bychain > undo > color zone #3 near #11 distance 8 > color #!11 byhetero [Repeated 1 time(s)] > ~heteroatom Unknown command: ~heteroatom > color zone #3 near #11 & protein distance 8 > color zone #3 near #11 distance 8 > color zone #3 near #11 & ~ligand & ~solvent distance 8 > color zone #3 near #11 & polymer distance 8 Expected a keyword > color #3 gray > color zone #3 near #11/A & protein distance 8 [Repeated 1 time(s)] > fitmap #11 inMap #3 Fit molecule 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11) to map combination of 2526 and 2540 emready2 (#3) using 8554 atoms average map value = 9.415, steps = 44 shifted from previous position = 0.244 rotated from previous position = 0.266 degrees atoms outside contour = 1045, contour level = 2.7111 Position of 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11) relative to combination of 2526 and 2540 emready2 (#3) coordinates: Matrix rotation and translation 0.96102761 0.09475034 0.25970812 -52.92644150 -0.27553875 0.25197696 0.92767775 31.87312977 0.02245732 -0.96308358 0.26826421 198.31177033 Axis -0.97400087 0.12221663 -0.19074956 Axis point 0.00000000 144.94453273 84.83756927 Rotation angle (degrees) 76.07601433 Shift along axis 17.61794287 > fitmap #11 inMap #3 Fit molecule 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11) to map combination of 2526 and 2540 emready2 (#3) using 8554 atoms average map value = 9.414, steps = 28 shifted from previous position = 0.00835 rotated from previous position = 0.0108 degrees atoms outside contour = 1042, contour level = 2.7111 Position of 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11) relative to combination of 2526 and 2540 emready2 (#3) coordinates: Matrix rotation and translation 0.96098510 0.09486625 0.25982307 -52.95701236 -0.27567867 0.25188266 0.92766179 31.90374037 0.02255887 -0.96309684 0.26820809 198.31213193 Axis -0.97397549 0.12222053 -0.19087665 Axis point 0.00000000 144.95021334 84.82634677 Rotation angle (degrees) 76.08170877 Shift along axis 17.62496843 > color #3 #b2ffffff models > color #3 #b2ffffc8 models > color #3 #b2ffffae models > color #3 #b2ffffaa models > color #3 #b2ffffab models > fitmap #11 inMap #3 Fit molecule 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11) to map combination of 2526 and 2540 emready2 (#3) using 8554 atoms average map value = 9.415, steps = 40 shifted from previous position = 0.00992 rotated from previous position = 0.0117 degrees atoms outside contour = 1047, contour level = 2.7111 Position of 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11) relative to combination of 2526 and 2540 emready2 (#3) coordinates: Matrix rotation and translation 0.96103238 0.09473372 0.25969653 -52.92173586 -0.27552298 0.25197233 0.92768369 31.87164356 0.02244658 -0.96308643 0.26825488 198.31472716 Axis -0.97400426 0.12221605 -0.19073265 Axis point 0.00000000 144.94452420 84.83909535 Rotation angle (degrees) 76.07628568 Shift along axis 17.61612817 > split #11 Split 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11) into 2 models Chain information for 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb A #11.1 --- Chain | Description A | No description available Chain information for 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb B #11.2 --- Chain | Description B | No description available > select add #11.1 6318 atoms, 6434 bonds, 824 residues, 1 model selected > select subtract #11.1 Nothing selected > select add #11.2 2236 atoms, 2278 bonds, 4 pseudobonds, 351 residues, 2 models selected > fitmap sel inMap #3 Fit molecule 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb B (#11.2) to map combination of 2526 and 2540 emready2 (#3) using 2236 atoms average map value = 7.606, steps = 52 shifted from previous position = 0.506 rotated from previous position = 1.99 degrees atoms outside contour = 454, contour level = 2.7111 Position of 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb B (#11.2) relative to combination of 2526 and 2540 emready2 (#3) coordinates: Matrix rotation and translation 0.95997604 0.12501582 0.25063329 -55.21416768 -0.27579491 0.26595891 0.92368989 30.40664271 0.04881769 -0.95584355 0.28979291 191.85480848 Axis -0.97266091 0.10443982 -0.20742005 Axis point 0.00000000 143.00817251 82.65941765 Rotation angle (degrees) 75.05664688 Shift along axis 17.08579253 > select add #11.1 8554 atoms, 8712 bonds, 4 pseudobonds, 1175 residues, 3 models selected > select subtract #11.2 6318 atoms, 6434 bonds, 824 residues, 1 model selected > fitmap sel inMap #3 Fit molecule 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb A (#11.1) to map combination of 2526 and 2540 emready2 (#3) using 6318 atoms average map value = 10.3, steps = 60 shifted from previous position = 0.0792 rotated from previous position = 0.218 degrees atoms outside contour = 516, contour level = 2.7111 Position of 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb A (#11.1) relative to combination of 2526 and 2540 emready2 (#3) coordinates: Matrix rotation and translation 0.96153052 0.09164231 0.25896090 -52.47900982 -0.27402598 0.25408547 0.92755072 31.47801921 0.01920469 -0.96283034 0.26942331 198.46339739 Axis -0.97427609 0.12356701 -0.18846035 Axis point 0.00000000 145.04029338 85.04809926 Rotation angle (degrees) 75.96470021 Shift along axis 17.61620776 > select subtract #11.1 Nothing selected > select add #11.1 6318 atoms, 6434 bonds, 824 residues, 1 model selected > select add #11.2 8554 atoms, 8712 bonds, 4 pseudobonds, 1175 residues, 3 models selected > combine sel > hide #!11 models > select add #11 8554 atoms, 8712 bonds, 4 pseudobonds, 1175 residues, 4 models selected > select subtract #11 Nothing selected > select subtract #14 Nothing selected > select ::name=""101"" 56 atoms, 60 bonds, 2 residues, 2 models selected > show sel & #!5 atoms > select clear > color zone #3 near #5 distance 8 [Repeated 1 time(s)] > undo [Repeated 1 time(s)] > select clear > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/open/vvd+iberdo open.pdb"" > models #5 relModel #3 > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/open/vvd+iberdo open.pdb"" Chain information for vvd+iberdo open.pdb #6 --- Chain | Description A | No description available B | No description available > mmaker #6 to #5 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker combination, chain A (#5) with vvd+iberdo open.pdb, chain A (#6), sequence alignment score = 4201.9 RMSD between 824 pruned atom pairs is 0.000 angstroms; (across all 824 pairs: 0.000) > hide #!5 models > color zone #3 near #6 distance 8 > color #3,6 byhetero > color #3,6 byelement > ui tool show ""Color Actions"" > color bychain > color bychain target cs [Repeated 1 time(s)] > color zone #3 near #6 distance 8 > select subtract #14 Nothing selected > hide #!6 models > show #!6 models > hide #!3 models > color #6/A:1-710 light blue > color #6/A:710-5000 steel blue > color #6/B:1-190 navajowhite > color #6/B:191-320 light salmon > color #6/B:321-500 tomato > select ::name=""101"" 84 atoms, 90 bonds, 3 residues, 3 models selected > color (#!6 & sel) lime > select clear > show #!3 models > fitmap #6 inMap #3 Fit molecule vvd+iberdo open.pdb (#6) to map combination of 2526 and 2540 emready2 (#3) using 8554 atoms average map value = 9.593, steps = 40 shifted from previous position = 0.000478 rotated from previous position = 0.00651 degrees atoms outside contour = 971, contour level = 2.7111 Position of vvd+iberdo open.pdb (#6) relative to combination of 2526 and 2540 emready2 (#3) coordinates: Matrix rotation and translation 0.99999490 0.00318409 0.00025382 -0.40275030 -0.00318393 0.99999473 -0.00063666 0.25133637 -0.00025585 0.00063585 0.99999976 -0.38480119 Axis 0.19535237 0.07824435 -0.97760691 Axis point 70.90279314 146.06118062 0.00000000 Rotation angle (degrees) 0.18660948 Shift along axis 0.31717173 > close #14 > color zone #3 near #6 distance 8 > hide #!3 models > show #!3 models > hide #!3 models > ui tool show ""Show Sequence Viewer"" > sequence chain #6/B Alignment identifier is 6/B > select #6/B:380 14 atoms, 15 bonds, 1 residue, 1 model selected > select #6/B:380 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select #6/B:386 14 atoms, 15 bonds, 1 residue, 1 model selected > select #6/B:386 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select #6/B:400 14 atoms, 15 bonds, 1 residue, 1 model selected > select #6/B:400 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select clear > show #!3 models > color #3 #b2ffff95 models > color #3 #b2ffff80 models > select add #6 8554 atoms, 8712 bonds, 4 pseudobonds, 1175 residues, 2 models selected > fitmap sel inMap #3 Fit molecule vvd+iberdo open.pdb (#6) to map combination of 2526 and 2540 emready2 (#3) using 8554 atoms average map value = 9.593, steps = 28 shifted from previous position = 0.00997 rotated from previous position = 0.00827 degrees atoms outside contour = 970, contour level = 2.7111 Position of vvd+iberdo open.pdb (#6) relative to combination of 2526 and 2540 emready2 (#3) coordinates: Matrix rotation and translation 0.99999451 0.00330818 0.00017995 -0.42084422 -0.00330806 0.99999432 -0.00063753 0.26238779 -0.00018206 0.00063693 0.99999978 -0.38918532 Axis 0.18887565 0.05365024 -0.98053436 Axis point 73.94006957 145.38881802 0.00000000 Rotation angle (degrees) 0.19330462 Shift along axis 0.31619952 > select clear > volume #3 level 1.638 > volume #3 level 1.191 > volume #3 level 1.861 > open 8W7 '8W7' has no suffix > open 8w7 '8w7' has no suffix > open PDB:8w7 PDB identifiers are either 4 or 8 characters long, got ""8w7"" > open ""/Users/zrizvi/Downloads/8W7 (1).cif"" Summary of feedback from opening /Users/zrizvi/Downloads/8W7 (1).cif --- warning | No mmCIF models found. > open ""/Users/zrizvi/Downloads/8W7 (1).cif"" Summary of feedback from opening /Users/zrizvi/Downloads/8W7 (1).cif --- warning | No mmCIF models found. > open ""/Users/zrizvi/Downloads/8W7 (1).cif"" Summary of feedback from opening /Users/zrizvi/Downloads/8W7 (1).cif --- warning | No mmCIF models found. > open ""/Users/zrizvi/Downloads/8W7 (1).cif"" Summary of feedback from opening /Users/zrizvi/Downloads/8W7 (1).cif --- warning | No mmCIF models found. > open ""/Users/zrizvi/Downloads/8W7 (1).cif"" Summary of feedback from opening /Users/zrizvi/Downloads/8W7 (1).cif --- warning | No mmCIF models found. > open 5v3o Summary of feedback from opening 5v3o fetched from pdb --- note | Fetching compressed mmCIF 5v3o from http://files.rcsb.org/download/5v3o.cif 5v3o title: Cereblon in complex with DDB1 and CC-220 [more info...] Chain information for 5v3o #7 --- Chain | Description | UniProt A | DNA damage-binding protein 1 | DDB1_HUMAN 1-1140 C | Protein cereblon | CRBN_HUMAN 40-442 Non-standard residues in 5v3o #7 --- 8W7 — (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione ZN — zinc ion > mmaker #7 to #6 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker vvd+iberdo open.pdb, chain A (#6) with 5v3o, chain A (#7), sequence alignment score = 3513.3 RMSD between 746 pruned atom pairs is 0.665 angstroms; (across all 775 pairs: 1.032) > hide #!3 models > select ::name=""8W7"" 33 atoms, 37 bonds, 1 residue, 1 model selected > color sel yellow > select clear > select #6/a 6318 atoms, 6434 bonds, 824 residues, 1 model selected > select #7/a/c 11175 atoms, 11396 bonds, 15 pseudobonds, 1452 residues, 3 models selected > select clear > split #7 Split 5v3o (#7) into 2 models Chain information for 5v3o A #7.1 --- Chain | Description A | No description available Chain information for 5v3o C #7.2 --- Chain | Description C | No description available > select add #7.1 8273 atoms, 8422 bonds, 9 pseudobonds, 1087 residues, 2 models selected > select subtract #7.1 Nothing selected > select add #7.2 2902 atoms, 2974 bonds, 6 pseudobonds, 365 residues, 3 models selected > select subtract #7.2 Nothing selected > hide #!6 models > split #7.2 Did not split 5v3o C, has only one piece Drag select of 1142 residues, 10 pseudobonds > delete sel Drag select of 162 residues, 5 pseudobonds > select up 1666 atoms, 1649 bonds, 5 pseudobonds, 212 residues, 4 models selected > select up 2415 atoms, 2431 bonds, 5 pseudobonds, 308 residues, 4 models selected > delete sel Drag select of 1 atoms > delete sel > show #!6 models > select add #7.2 33 atoms, 37 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #7.2,0.38926,0.71182,0.58463,95.207,-0.9138,0.3783,0.14783,121.63,-0.11594,-0.59178,0.79772,151.44 > ui mousemode right translate > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #7.2,0.38926,0.71182,0.58463,96.147,-0.9138,0.3783,0.14783,122.74,-0.11594,-0.59178,0.79772,154.04 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #7.2,0.38926,0.71182,0.58463,95.535,-0.9138,0.3783,0.14783,118.94,-0.11594,-0.59178,0.79772,152.93 > ui mousemode right ""rotate selected models"" > view matrix models > #7.2,0.58527,0.4424,0.67952,103.57,-0.3231,-0.64138,0.69587,163.23,0.74369,-0.62682,-0.23244,77.254 > ui mousemode right ""translate selected models"" > view matrix models > #7.2,0.58527,0.4424,0.67952,102.52,-0.3231,-0.64138,0.69587,162.38,0.74369,-0.62682,-0.23244,77.227 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #7.2,0.58527,0.4424,0.67952,102.28,-0.3231,-0.64138,0.69587,162.87,0.74369,-0.62682,-0.23244,77.81 > ui mousemode right ""rotate selected models"" > view matrix models > #7.2,0.49337,0.54152,0.68069,101.54,-0.38847,-0.56301,0.72946,163.07,0.77825,-0.62432,-0.067408,81.726 > ui mousemode right ""translate selected models"" > view matrix models > #7.2,0.49337,0.54152,0.68069,100.97,-0.38847,-0.56301,0.72946,163.71,0.77825,-0.62432,-0.067408,82.414 > ui mousemode right translate > show #!3 models > ui mousemode right ""translate selected models"" > view matrix models > #7.2,0.49337,0.54152,0.68069,101.48,-0.38847,-0.56301,0.72946,162.04,0.77825,-0.62432,-0.067408,81.359 > ui mousemode right translate > select subtract #7.2 Nothing selected > select add #7.2 33 atoms, 37 bonds, 1 residue, 1 model selected > fitmap sel inMap #3 Fit molecule 5v3o C (#7.2) to map combination of 2526 and 2540 emready2 (#3) using 33 atoms average map value = 5.737, steps = 256 shifted from previous position = 7.36 rotated from previous position = 81 degrees atoms outside contour = 3, contour level = 1.8614 Position of 5v3o C (#7.2) relative to combination of 2526 and 2540 emready2 (#3) coordinates: Matrix rotation and translation 0.87027007 -0.19554474 -0.45209762 50.53821845 -0.20191453 -0.97878910 0.03467589 165.49997848 -0.44928891 0.06110769 -0.89129418 123.26330988 Axis 0.96702224 -0.10275818 -0.23304237 Axis point 0.00000000 84.99703244 68.30715524 Rotation angle (degrees) 179.21693737 Shift along axis 3.13952962 > select clear > select add #7.2 33 atoms, 37 bonds, 1 residue, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #7.2,-0.13555,0.48062,0.86639,135.27,-0.89289,-0.43824,0.10341,162.86,0.42939,-0.75958,0.48854,124.48 > ui mousemode right ""translate selected models"" > view matrix models > #7.2,-0.13555,0.48062,0.86639,141.75,-0.89289,-0.43824,0.10341,158.53,0.42939,-0.75958,0.48854,124.12 > select clear > select add #7.2 33 atoms, 37 bonds, 1 residue, 1 model selected > view matrix models > #7.2,-0.13555,0.48062,0.86639,141.75,-0.89289,-0.43824,0.10341,158.95,0.42939,-0.75958,0.48854,124.57 > ui mousemode right translate > select clear > select add #7.2 33 atoms, 37 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #7.2,-0.13555,0.48062,0.86639,141.5,-0.89289,-0.43824,0.10341,158.01,0.42939,-0.75958,0.48854,123.53 > select subtract #7.2 Nothing selected > ui mousemode right translate > select add #6 8554 atoms, 8712 bonds, 4 pseudobonds, 1175 residues, 2 models selected > select add #7.2 8587 atoms, 8749 bonds, 4 pseudobonds, 1176 residues, 3 models selected > combine sel > rename #8 ""vvd+iberdo open.pdb"" > close #6 > close #7 > select ::name=""8W7"" 33 atoms, 37 bonds, 1 residue, 1 model selected > color sel lime > ui tool show ""Show Sequence Viewer"" > sequence chain #8/B Alignment identifier is 8/B > select #8/B:380 14 atoms, 15 bonds, 1 residue, 1 model selected > select #8/B:380 14 atoms, 15 bonds, 1 residue, 1 model selected > hide sel atoms > select #8/B:386 14 atoms, 15 bonds, 1 residue, 1 model selected > select #8/B:386 14 atoms, 15 bonds, 1 residue, 1 model selected > hide sel atoms > select #8/B:400 14 atoms, 15 bonds, 1 residue, 1 model selected > select #8/B:400 14 atoms, 15 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > color zone #3 near #8 distance 8 > hide #!8 models > show #!8 models > color #3 #b2ffff80 models > split #8 Split vvd+iberdo open.pdb (#8) into 3 models Chain information for vvd+iberdo open.pdb A #8.1 --- Chain | Description A | No description available Chain information for vvd+iberdo open.pdb B #8.2 --- Chain | Description B | No description available > select add #8.3 33 atoms, 37 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #8.3,0.96286,-0.26914,0.021531,52.392,0.092796,0.25499,-0.96248,184.87,0.25355,0.92873,0.2705,-69.001 > select clear > select add #8.3 33 atoms, 37 bonds, 1 residue, 1 model selected > view matrix models > #8.3,0.96286,-0.26914,0.021531,54.262,0.092796,0.25499,-0.96248,185.23,0.25355,0.92873,0.2705,-68.133 > ui mousemode right ""rotate selected models"" > view matrix models > #8.3,0.86549,-0.29977,0.40134,13.855,0.49866,0.59184,-0.6333,63.657,-0.047687,0.74824,0.66171,-74.281 > ui mousemode right ""translate selected models"" > view matrix models > #8.3,0.86549,-0.29977,0.40134,12.593,0.49866,0.59184,-0.6333,65.975,-0.047687,0.74824,0.66171,-72.26 > ui mousemode right translate > select add #8 8587 atoms, 8749 bonds, 4 pseudobonds, 1176 residues, 5 models selected > combine sel > select subtract #8 Nothing selected > hide #!8 models > hide #!6 models > show #!6 models > rename #6 ""vvd+iberdo open.pdb"" > close #8 > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!6 models > show #!5 models > close #5 > show #!6 models > color zone #3 near #6 distance 8 > hide #!6 models > ui mousemode right ""pick blobs"" > measure blob #!3.1 triangleNumber 951490 color #ff6b4dff Surface combination of 2526 and 2540 emready2 #3.1 blob: volume = 1.0432e+05 area = 80715 size = 105.54 83.9 82.228 > undo > select add #6 8587 atoms, 8749 bonds, 4 pseudobonds, 1176 residues, 2 models selected > copy sel Unknown command: copy sel > select clear Drag select of 5 atoms, 7 bonds > select up 8 atoms, 8 bonds, 1 residue, 1 model selected > select ::name=""8W7"" 33 atoms, 37 bonds, 1 residue, 1 model selected > color sel yellow > select clear Drag select of 7 atoms, 7 bonds > delete sel Drag select of 4 atoms, 6 bonds > delete sel Drag select of 1 atoms > delete sel Drag select of 1 atoms > delete sel Drag select of 2 atoms, 1 bonds > delete sel > select ::name=""8W7"" 18 atoms, 20 bonds, 1 residue, 1 model selected > color sel lime > color zone #3 near #6 distance 8 > select add #6 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 2 models selected > select subtract #6 Nothing selected > hide #!6 models > graphics silhouettes true > lighting shadows false > lighting soft > volume #3 level 2.487 > volume #3 level 4.142 > volume #3 level 2.353 > volume #3 level 1.861 > volume #3 level 2.085 > volume #3 level 2.264 > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/fig2b.open.png"" width 1800 > height 1532 supersample 4 transparentBackground true > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/open/vvd+iberdo open.pdb"" Chain information for vvd+iberdo open.pdb #5 --- Chain | Description A | No description available B | No description available > hide #!3 models > close #5 > show #!6 models > show #!3 models > save vvd+iberdo open.pdb #6 Cannot determine format for 'vvd+iberdo' > save vvd+iberdo_open.pdb #6 > open /Users/zrizvi/Desktop/vvd+iberdo_open.pdb Chain information for vvd+iberdo_open.pdb #5 --- Chain | Description A | No description available B | No description available > hide #!6 models > hide #!3 models > close #5 > show #!3 models > rename #9 ""1. cryosparc_P341_J1735_NUrefine selected.mrc"" > rename #4 ""2. cryosparc_P341_J1614_localrefine. selected.mrc"" > rename #10 ""3. composite_map on EMReady2 maps of 1735 and 1614.ccp4"" > show #!10 models > hide #!3 models > show #!13 models > rename #10 ""3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4"" > rename #13 ""3b. composite_map on EMReady2 maps of 1735 and 1614.ccp4 split"" > rename #1 ""4. open- vvd+imid NU J2526_map_emready2.mrc"" > rename #2 ""5. open- vvd+imid local J2540_005_volume_map_emready2.mrc"" > rename #3 ""6. combination of 2526 and 2540 emready2"" > rename #11 ""3c. 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb"" > rename #3 ""6a. combination of 2526 and 2540 emready2"" > rename #6 ""6b. vvd+iberdo open.pdb"" > hide #!10 models > hide #!13 models > show #!3 models > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig > maps/closed/J2528_map_emready2.mrc"" Opened J2528_map_emready2.mrc as #5, grid size 443,443,443, pixel 0.5, shown at level 1.11, step 2, values float32 > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig > maps/closed/J2544_007_volume_map_emready2.mrc"" Opened J2544_007_volume_map_emready2.mrc as #7, grid size 443,443,443, pixel 0.5, shown at level 0.445, step 2, values float32 > hide #!3 models > show #!3 models > hide #!3 models > hide #!5 models > show #!5 models > rename #5 ""7. J2528_map_emready2.mrc"" > rename #7 ""8. J2544_007_volume_map_emready2.mrc"" > vop max #5 #7 Opened volume maximum as #8, grid size 443,443,443, pixel 0.5, shown at step 1, values float32 > rename #8 ""9. combination of 2528 and 2544 emready2"" > rename #5 ""7. Clsoed- vvd+imid NU J2528_map_emready2.mrc"" > rename #7 ""8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc"" > volume #8 level 2.891 > volume #8 level 3.239 > show #!5 models > hide #!8 models > volume #5 level 1.869 > volume #5 step 1 > volume #7 step 1 > volume #5 level 2.307 > volume #7 level 2.027 > volume #8 level 4.502 > open 8w7 '8w7' has no suffix > open 5v3o 5v3o title: Cereblon in complex with DDB1 and CC-220 [more info...] Chain information for 5v3o #14 --- Chain | Description | UniProt A | DNA damage-binding protein 1 | DDB1_HUMAN 1-1140 C | Protein cereblon | CRBN_HUMAN 40-442 Non-standard residues in 5v3o #14 --- 8W7 — (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione ZN — zinc ion > view > select add #14 11175 atoms, 11396 bonds, 15 pseudobonds, 1452 residues, 4 models selected > ui mousemode right ""translate selected models"" > view matrix models #14,1,0,0,48.358,0,1,0,11.289,0,0,1,14.423 > view matrix models > #14,0.31895,0.61517,0.72099,49.34,-0.57201,-0.48161,0.66397,53.169,0.75569,-0.62419,0.19828,12.134 > view matrix models > #14,0.31895,0.61517,0.72099,159.92,-0.57201,-0.48161,0.66397,132.09,0.75569,-0.62419,0.19828,22.744 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #14,0.31895,0.61517,0.72099,155.88,-0.57201,-0.48161,0.66397,192.02,0.75569,-0.62419,0.19828,124.04 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #14,0.31895,0.61517,0.72099,115.83,-0.57201,-0.48161,0.66397,174.7,0.75569,-0.62419,0.19828,127.25 > fitmap #14 inMap #8 Fit molecule 5v3o (#14) to map 9. combination of 2528 and 2544 emready2 (#8) using 11175 atoms average map value = 7.021, steps = 152 shifted from previous position = 3.28 rotated from previous position = 10.9 degrees atoms outside contour = 4670, contour level = 4.502 Position of 5v3o (#14) relative to 9. combination of 2528 and 2544 emready2 (#8) coordinates: Matrix rotation and translation 0.26528196 0.56680440 0.77997325 120.97229633 -0.46678619 -0.63233295 0.61827640 177.51482496 0.84364456 -0.52809831 0.09682995 121.14258530 Axis -0.74206572 -0.04121541 -0.66905885 Axis point 0.00000000 86.02124003 -48.12980321 Rotation angle (degrees) 129.42818226 Shift along axis -178.13725982 > select clear > hide #!8 models Drag select of 307 residues, 1 pseudobonds > delete sel Drag select of 5 residues, 2 pseudobonds > delete sel > show #!8 models > hide #!14.2 models > split #14 Split 5v3o (#14) into 2 models Chain information for 5v3o A #14.1 --- Chain | Description A | No description available Chain information for 5v3o C #14.2 --- Chain | Description C | No description available > select add #14.1 5977 atoms, 6081 bonds, 10 pseudobonds, 775 residues, 2 models selected > fitmap sel inMap #8 Fit molecule 5v3o A (#14.1) to map 9. combination of 2528 and 2544 emready2 (#8) using 5977 atoms average map value = 10.5, steps = 48 shifted from previous position = 0.0818 rotated from previous position = 0.0954 degrees atoms outside contour = 859, contour level = 4.502 Position of 5v3o A (#14.1) relative to 9. combination of 2528 and 2544 emready2 (#8) coordinates: Matrix rotation and translation 0.26556282 0.56807609 0.77895183 120.93900210 -0.46621575 -0.63154059 0.61951543 177.60964780 0.84387160 -0.52767987 0.09713232 121.11920711 Axis -0.74205410 -0.04199283 -0.66902340 Axis point 0.00000000 85.98100831 -48.17253109 Rotation angle (degrees) 129.37718193 Shift along axis -178.23319887 > select subtract #14.1 Nothing selected > select add #14.2 2902 atoms, 2974 bonds, 6 pseudobonds, 365 residues, 3 models selected > fitmap sel inMap #8 Fit molecule 5v3o C (#14.2) to map 9. combination of 2528 and 2544 emready2 (#8) using 2902 atoms average map value = 6.215, steps = 148 shifted from previous position = 0.846 rotated from previous position = 5.97 degrees atoms outside contour = 1226, contour level = 4.502 Position of 5v3o C (#14.2) relative to 9. combination of 2528 and 2544 emready2 (#8) coordinates: Matrix rotation and translation 0.32722427 0.49885846 0.80253631 122.38342857 -0.43918680 -0.67169932 0.59660287 176.79079036 0.83668347 -0.54768629 -0.00070427 118.63599032 Axis -0.77315201 -0.02307192 -0.63380096 Axis point 0.00000000 88.97949673 -40.28109264 Rotation angle (degrees) 132.26725177 Shift along axis -173.89150166 > select clear > select add #14 8879 atoms, 9055 bonds, 16 pseudobonds, 1140 residues, 6 models selected > combine sel > close #14 > rename #15 ""9b. "" > rename #15 ""9b. 5v3o- closed vvd+imid"" > color #15/A:1-710 light blue > hide #!8 models > color #15/A:710-5000 steel blue > color #15/B:1-190 navajowhite > color #15/C:1-190 navajowhite > color #15/C:191-320 light salmon > color #15/C:321-500 tomato > select clear > select ::name=""8W7"" 51 atoms, 57 bonds, 2 residues, 2 models selected > color (#!15 & sel) lime > select clear > show #!8 models > color #8 #ffb2b2a1 models > select #15/C:287 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select clear > volume #8 level 5.503 > color zone #8 near #15 distance 8 > hide #!15 models > show #!15 models > hide #!8 models > show #!8 models > color #8 #ffb2b29c models > volume #8 level 2.935 > volume #8 level 5.547 > ui tool show ""Side View"" > hide #!8 models > select #15/C:377 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 68 atoms, 72 bonds, 8 residues, 1 model selected > show sel atoms > select clear > show #!8 models > color zone #8 near #15 distance 8 > hide #!15 models > volume #8 level 4.023 > volume #8 level 5.547 > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/closed/fig2b.closed.png"" > width 1800 height 1532 supersample 4 transparentBackground true > volume #8 level 4.807 > volume #8 level 1.672 > volume #8 level 2.107 > volume #8 level 3.109 > color zone #8 near #15 distance 10 > volume #8 level 5.068 > rename #8 ""9a. combination of 2528 and 2544 emready2"" > hide #!8 models > show #!6 models > show #!3 models > hide #!6 models > volume #3 level 6.557 > volume #3 level 3.829 > volume #3 level 2.04 > volume #3 level 3.069 > volume #3 level 4.053 > volume copy #3 modelId #16 Opened 6a. combination of 2526 and 2540 emready2 copy as #16, grid size 443,443,443, pixel 0.5, shown at step 1, values float32 > show #!3 models > hide #!16 models > show #!16 models > hide #!3 models > color #16 #b2ffffff models > show #!6 models > color zone #16 near #6 distance 10 > hide #!16 models > show #!16 models > hide #!6 models > rename #16 ""6b. combination of 2526 and 2540 emready2 copy"" > rename #6 ""6c. vvd+iberdo open.pdb"" > volume #16 level 2.622 > volume #16 level 2.174 > show #!3 models > hide #!16 models > volume #3 level 6.557 > show #!16 models > hide #!16 models > volume #3 level 5.26 > volume #3 level 4.41 > volume #3 level 4.321 > volume #3 level 6.02 > show #!6 models > ui tool show ""Map Eraser"" > ui tool show ""Segment Map"" > select add #6 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 2 models selected > select subtract #6 Nothing selected > ui tool show ""Color Zone"" > volume splitbyzone #3 Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 > hide #!14.8 models > show #!14.8 models > hide #!14.7 models > show #!14.7 models > hide #!14.7 models > show #!14.7 models > hide #!14.8 models > hide #!14.7 models > hide #!14.6 models > hide #!14.5 models > hide #!14.4 models > select add #14.1 2 models selected > select add #14.2 4 models selected > select add #14.3 6 models selected > select subtract #14.3 4 models selected > select subtract #14.2 2 models selected > select subtract #14.1 Nothing selected > show #!16 models > hide #!14 models > hide #!14.1 models > hide #!14.2 models > hide #!14.3 models > show #!14.3 models > show #!14.2 models > show #!14.1 models > hide #!14 models > volume splitbyzone #16 Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 > hide #!17.1 models > hide #!17.2 models > hide #!17.3 models > hide #!17.4 models > show #!17.4 models > hide #!17.5 models > show #!17.5 models > show #!14 models > hide #!6 models > hide #!17.5 models > show #!17.5 models > hide #!17.5 models > show #!17.5 models > hide #!17.6 models > show #!17.6 models > hide #!17.6 models > show #!17.6 models > hide #!17.7 models > show #!17.7 models > volume #17.4 level 2.889 > volume #17.5 level 2.842 > volume #17.6 level 2.849 > volume #17.8 level 2.108 > volume #14.8 level 6.219 > select add #14 17 models selected > select subtract #14.4 15 models selected > select subtract #14.5 13 models selected > select subtract #14.6 11 models selected > select subtract #14.7 9 models selected > select subtract #14.8 7 models selected > hide #!14.8 models > select add #17.4 9 models selected > select add #17.5 11 models selected > select add #17.6 13 models selected > select add #17.7 15 models selected > select add #17.8 17 models selected > combine sel No structures specified > select clear > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/open/fig2b.open.png"" width > 1800 height 1802 supersample 4 transparentBackground true > hide #!14 models > hide #!17 models > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/figure 2 making .cxs"" > includeMaps true > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/int > 1/J2527_map_emready2.mrc"" Opened J2527_map_emready2.mrc as #18, grid size 443,443,443, pixel 0.5, shown at level 0.9, step 2, values float32 > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/int > 1/J2541_004_volume_map_emready2.mrc"" Opened J2541_004_volume_map_emready2.mrc as #19, grid size 443,443,443, pixel 0.5, shown at level 1.16, step 2, values float32 > volume #18 step 1 > volume #19 step 1 > vop max #18 #19 Opened volume maximum as #20, grid size 443,443,443, pixel 0.5, shown at step 1, values float32 > rename #18 ""10. int1 vvd+imid J2527_map_emready2.mrc"" > rename #19 ""11. int1 vvd+imid localJ2541_004_volume_map_emready2.mrc"" > rename #19 ""11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc"" > rename #18 ""10. int1 vvd+imid NU J2527_map_emready2.mrc"" > rename #20 ""12. combination of 10 and 11"" > volume #20 level 2.786 > show #!6 models > hide #!6 models > volume copy #6 modelId #21 > combine #6 close false modelId #21 > rename #21 ""13. vvd+iberdo int1.pdb"" > volume #20 level 3.94 > select add #21 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #21,0.97808,0.10952,0.17709,-17.951,-0.12509,0.98898,0.079242,-5.2311,-0.16646,-0.099657,0.981,45.059 > ui mousemode right ""translate selected models"" > view matrix models > #21,0.97808,0.10952,0.17709,-30.302,-0.12509,0.98898,0.079242,8.1696,-0.16646,-0.099657,0.981,35.267 > ui mousemode right translate > fitmap #21 inMap #20 Fit molecule 13. vvd+iberdo int1.pdb (#21) to map 12. combination of 10 and 11 (#20) using 8572 atoms average map value = 10.14, steps = 156 shifted from previous position = 3.61 rotated from previous position = 13.7 degrees atoms outside contour = 1471, contour level = 3.9404 Position of 13. vvd+iberdo int1.pdb (#21) relative to 12. combination of 10 and 11 (#20) coordinates: Matrix rotation and translation 0.99995221 -0.00495979 0.00842498 -0.14657304 0.00521895 0.99950504 -0.03102311 2.46328273 -0.00826694 0.03106560 0.99948316 -4.02043145 Axis 0.95383084 0.25642777 0.15636984 Axis point 0.00000000 130.03408034 78.45787904 Rotation angle (degrees) 1.86513633 Shift along axis -0.13682601 > split #21 Split 13. vvd+iberdo int1.pdb (#21) into 3 models Chain information for 13. vvd+iberdo int1.pdb A #21.1 --- Chain | Description A | No description available Chain information for 13. vvd+iberdo int1.pdb B #21.2 --- Chain | Description B | No description available > select add #21.1 6318 atoms, 6434 bonds, 824 residues, 1 model selected > fitmap sel inMap #20 Fit molecule 13. vvd+iberdo int1.pdb A (#21.1) to map 12. combination of 10 and 11 (#20) using 6318 atoms average map value = 11.2, steps = 64 shifted from previous position = 0.057 rotated from previous position = 0.261 degrees atoms outside contour = 716, contour level = 3.9404 Position of 13. vvd+iberdo int1.pdb A (#21.1) relative to 12. combination of 10 and 11 (#20) coordinates: Matrix rotation and translation 0.99997710 -0.00370364 0.00566496 -0.04489164 0.00385882 0.99961071 -0.02763236 2.26194806 -0.00556041 0.02765359 0.99960210 -3.76505421 Axis 0.97131472 0.19721768 0.13286424 Axis point 0.00000000 136.84114012 80.62843893 Rotation angle (degrees) 1.63082033 Shift along axis -0.09774884 > select subtract #21.1 Nothing selected > select add #21.2 2236 atoms, 2278 bonds, 4 pseudobonds, 351 residues, 2 models selected > fitmap sel inMap #20 Fit molecule 13. vvd+iberdo int1.pdb B (#21.2) to map 12. combination of 10 and 11 (#20) using 2236 atoms average map value = 7.656, steps = 72 shifted from previous position = 0.362 rotated from previous position = 1.2 degrees atoms outside contour = 705, contour level = 3.9404 Position of 13. vvd+iberdo int1.pdb B (#21.2) relative to 12. combination of 10 and 11 (#20) coordinates: Matrix rotation and translation 0.99957428 -0.00690597 0.02834733 -2.14892969 0.00760810 0.99966507 -0.02473610 1.22829977 -0.02816701 0.02494124 0.99929203 -1.15331989 Axis 0.64826372 0.73748312 0.18940116 Axis point -37.68629592 0.00000000 59.10362530 Rotation angle (degrees) 2.19586462 Shift along axis -0.70566292 > select subtract #21.2 Nothing selected > select add #21.3 18 atoms, 20 bonds, 1 residue, 1 model selected > fitmap sel inMap #20 Fit molecule 13. vvd+iberdo int1.pdb C (#21.3) to map 12. combination of 10 and 11 (#20) using 18 atoms average map value = 4.502, steps = 88 shifted from previous position = 2.28 rotated from previous position = 28.1 degrees atoms outside contour = 6, contour level = 3.9404 Position of 13. vvd+iberdo int1.pdb C (#21.3) relative to 12. combination of 10 and 11 (#20) coordinates: Matrix rotation and translation 0.88481403 0.46470450 -0.03396844 -31.04162349 -0.46574688 0.88420785 -0.03544474 62.18114561 0.01356383 0.04718270 0.99879418 -9.42993675 Axis 0.08834121 -0.05081918 -0.99479307 Axis point 110.31812113 94.80438715 0.00000000 Rotation angle (degrees) 27.88255888 Shift along axis 3.47858654 > select subtract #21.3 Nothing selected > select add #21 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 5 models selected > combine sel > rename #22 ""13. vvd+iberdo int1.pdb"" > close #21 > volume #20 level 3.094 > volume #20 level 1.785 > volume #20 level 0.3997 > volume #20 level 0.6692 > volume #20 level 3.286 > color zone #20 near #22 distance 10 > hide #!20 models > ui tool show ""Show Sequence Viewer"" > sequence chain #22/B Alignment identifier is 22/B > select #22/B:304-380 364 atoms, 365 bonds, 61 residues, 1 model selected > select #22/B:304-380 364 atoms, 365 bonds, 61 residues, 1 model selected > select #22/B:380 14 atoms, 15 bonds, 1 residue, 1 model selected > select #22/B:380 14 atoms, 15 bonds, 1 residue, 1 model selected > select #22/B:386 14 atoms, 15 bonds, 1 residue, 1 model selected > select #22/B:386 14 atoms, 15 bonds, 1 residue, 1 model selected > select #22/B:400 14 atoms, 15 bonds, 1 residue, 1 model selected > select #22/B:400 14 atoms, 15 bonds, 1 residue, 1 model selected > select clear > select #22/B:380 14 atoms, 15 bonds, 1 residue, 1 model selected > select #22/B:380 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select #22/B:385-386 19 atoms, 20 bonds, 2 residues, 1 model selected > select #22/B:385-386 19 atoms, 20 bonds, 2 residues, 1 model selected > select #22/B:386 14 atoms, 15 bonds, 1 residue, 1 model selected > select #22/B:386 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select #22/B:400 14 atoms, 15 bonds, 1 residue, 1 model selected > select #22/B:400 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select ::name=""8W7"" 69 atoms, 77 bonds, 3 residues, 3 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.98816,-0.15319,0.0089352,36.88,0.054684,0.29714,-0.95327,185.4,0.14337,0.94246,0.302,-62.636,#15,0.33655,0.47781,0.81144,123.71,-0.45116,-0.67455,0.58433,177.73,0.82655,-0.56275,-0.011449,119.32,#22,0.99241,0.043403,0.11506,-17.961,-0.044168,0.99902,0.0041065,4.463,-0.11476,-0.0091571,0.99335,14.959 > undo > ui mousemode right translate > select add #22 8623 atoms, 8789 bonds, 4 pseudobonds, 1178 residues, 4 models selected > select subtract #22 51 atoms, 57 bonds, 2 residues, 2 models selected > hide #!22 models > show #!22 models > show #!20 models > split #22 Split 13. vvd+iberdo int1.pdb (#22) into 3 models Chain information for 13. vvd+iberdo int1.pdb A #22.1 --- Chain | Description A | No description available Chain information for 13. vvd+iberdo int1.pdb B #22.2 --- Chain | Description B | No description available > select add #22.3 69 atoms, 77 bonds, 3 residues, 3 models selected > hide #!20 models > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.45288,-0.60813,0.65198,63.103,0.65358,-0.27093,-0.7067,186.66,0.60641,0.74617,0.27477,-71.309,#15,0.27736,0.96074,-0.0072709,59.877,-0.36454,0.11224,0.9244,172.73,0.88892,-0.25374,0.38136,129.94,#22.3,0.61242,-0.75011,-0.24956,149.65,0.69113,0.66128,-0.29162,6.4196,0.38378,0.0061171,0.9234,-29.009 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.45288,-0.60813,0.65198,66.626,0.65358,-0.27093,-0.7067,185.57,0.60641,0.74617,0.27477,-70.936,#15,0.27736,0.96074,-0.0072709,63.4,-0.36454,0.11224,0.9244,171.63,0.88892,-0.25374,0.38136,130.31,#22.3,0.61242,-0.75011,-0.24956,153.17,0.69113,0.66128,-0.29162,5.324,0.38378,0.0061171,0.9234,-28.635 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #6,0.45288,-0.60813,0.65198,66.315,0.65358,-0.27093,-0.7067,185.29,0.60641,0.74617,0.27477,-70.511,#15,0.27736,0.96074,-0.0072709,63.089,-0.36454,0.11224,0.9244,171.35,0.88892,-0.25374,0.38136,130.74,#22.3,0.61242,-0.75011,-0.24956,152.86,0.69113,0.66128,-0.29162,5.0465,0.38378,0.0061171,0.9234,-28.21 > ui mousemode right translate > show #!20 models > hide #!20 models > select add #22 8623 atoms, 8789 bonds, 4 pseudobonds, 1178 residues, 7 models selected > combine sel Remapping chain ID 'A' in 9b. 5v3o- closed vvd+imid #15 to 'D' Remapping chain ID 'C' in 9b. 5v3o- closed vvd+imid #15 to 'E' Remapping chain ID 'A' in 13. vvd+iberdo int1.pdb A #22.1 to 'F' Remapping chain ID 'B' in 13. vvd+iberdo int1.pdb B #22.2 to 'G' Remapping chain ID 'C' in 13. vvd+iberdo int1.pdb C #22.3 to 'H' > rename #21 ""13. vvd+iberdo int1.pdb"" > close #22 > select add #15 8897 atoms, 9075 bonds, 16 pseudobonds, 1141 residues, 4 models selected > select subtract #15 18 atoms, 20 bonds, 1 residue, 1 model selected > select add #6 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 2 models selected > select subtract #6 Nothing selected > show #!20 models > split #13 > hide #21.2 models > show #21.2 models > hide #21.2 models > show #21.2 models > split #21 Split 13. vvd+iberdo int1.pdb (#21) into 8 models Chain information for 13. vvd+iberdo int1.pdb A #21.1 --- Chain | Description A | No description available Chain information for 13. vvd+iberdo int1.pdb B #21.2 --- Chain | Description B | No description available Chain information for 13. vvd+iberdo int1.pdb D #21.4 --- Chain | Description D | No description available Chain information for 13. vvd+iberdo int1.pdb E #21.5 --- Chain | Description E | No description available Chain information for 13. vvd+iberdo int1.pdb F #21.6 --- Chain | Description F | No description available Chain information for 13. vvd+iberdo int1.pdb G #21.7 --- Chain | Description G | No description available Cell requested for row 20 is out of bounds for table with 35 rows! Resizing table model. > ~split #13 Unknown command: ~split #13 > hide #!21 models > show #!21 models > hide #21.1 models > show #21.1 models > hide #21.1 models > hide #!21.2 models > hide #21.3 models > hide #!21.4 models > hide #!21.5 models > hide #21.6 models > show #21.6 models > hide #!21.7 models > show #!21.7 models > hide #21.8 models > show #21.8 models > close #21.1,3#21.2,4-5 > hide #!21 models > show #!21 models > hide #!20 models > select add #21.6 6318 atoms, 6434 bonds, 824 residues, 1 model selected > select add #21.7 8554 atoms, 8712 bonds, 4 pseudobonds, 1175 residues, 3 models selected > select add #21.8 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 4 models selected > combine sel > rename #22 ""13. vvd+iberdo int1.pdb"" > close #21 > show #!20 models > color zone #20 near #22 distance 10 > color zone #20 near #22 distance 8 > hide #!22 models > volume #20 level 1.554 > volume #20 level 0.05338 > volume #20 level 0.5922 > volume #20 level 0.7461 > volume #20 level 0.8616 > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"" > includeMaps true ——— End of log from Tue Feb 24 16:13:45 2026 ——— > view name session-start opened ChimeraX session OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M4 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,1 Model Number: MW2V3LL/A Chip: Apple M4 Total Number of Cores: 10 (4 performance and 6 efficiency) Memory: 16 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6.1 (24G90) Kernel Version: Darwin 24.6.0 Time since boot: 4 days, 23 hours, 9 minutes Graphics/Displays: Apple M4: Chipset Model: Apple M4 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U3011: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.2.0 autocommand: 2.2.2 babel: 2.17.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.2.0 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.1 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.19.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.1 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.5 ChimeraX-AtomicLibrary: 14.1.13 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 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-Clipper: 0.23.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.dev202503130118 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 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-ISOLDE: 1.8.dev0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.5.1 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: 2.1.7 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: 2.15 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: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.7 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-ProfileGrids: 1.0.2 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 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: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17 ChimeraX-Shape: 1.1 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: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.44 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 coverage: 7.6.12 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.13 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.17.0 fonttools: 4.56.0 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h5py: 3.13.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 inflect: 7.3.1 iniconfig: 2.0.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.collections: 5.1.0 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 msgpack: 1.1.0 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 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 pluggy: 1.5.0 prompt_toolkit: 3.0.50 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: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.1 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.3.5 pytest-cov: 6.0.0 python-dateutil: 2.9.0.post0 pytz: 2025.1 pyzmq: 26.3.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 Send2Trash: 1.8.3 SEQCROW: 1.8.21 setuptools: 75.8.2 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2025.1 urllib3: 2.3.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel: 0.43.0 wheel-filename: 1.4.2 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect closed normal Window Toolkit duplicate all ChimeraX