![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 days ago
Closed 35 hours ago
#19902 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
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. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
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"uptime" : 91000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac16,1",
"coalitionID" : 2752,
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"build" : "24G90",
"releaseType" : "User"
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"captureTime" : "2026-02-24 16:39:48.1591 -0800",
"codeSigningMonitor" : 2,
"incident" : "F12726C2-043C-463E-B315-8C2C8621A4A0",
"pid" : 24683,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-02-23 15:51:11.7404 -0800",
"procStartAbsTime" : 1767101685521,
"procExitAbsTime" : 2190221507183,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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"crashReporterKey" : "E2796449-E3BF-8B60-EBDE-A5CD5F936DBB",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
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Address size fault"},"pc":{"value":6835088236},"far":{"value":0}}},{"id":1706011,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":217}],"threadState":{"x":[{"value":13999501312},{"value":247223},{"value":13998964736},{"value":13999500160},{"value":5193732},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":0},"fp":{"value":0},"sp":{"value":13999500144},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6835088236},"far":{"value":0}}},{"id":1711202,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":217}],"threadState":{"x":[{"value":13518057472},{"value":170939},{"value":13517520896},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":0},"fp":{"value":0},"sp":{"value":13518057472},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6835088236},"far":{"value":0}}},{"id":1711203,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":217}],"threadState":{"x":[{"value":13524348928},{"value":174675},{"value":13523812352},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":0},"fp":{"value":0},"sp":{"value":13524348928},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6835088236},"far":{"value":0}}},{"id":1711204,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":217}],"threadState":{"x":[{"value":13585018880},{"value":246575},{"value":13584482304},{"value":13585017728},{"value":5193732},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":0},"fp":{"value":0},"sp":{"value":13585017712},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6835088236},"far":{"value":0}}},{"id":1711205,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":217}],"threadState":{"x":[{"value":13514846208},{"value":109603},{"value":13514309632},{"value":13514845056},{"value":5193732},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":0},"fp":{"value":0},"sp":{"value":13514845040},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6835088236},"far":{"value":0}}}],
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Log:
UCSF 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/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
Change History (2)
comment:1 by , 39 hours ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 35 hours ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
This ChimeraX crash is in the Qt window toolkit and happens on Macs when waking from sleep or with multiple displays. We have not seen it in the newer ChimeraX 1.11 which uses a newer Qt window toolkit.
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Reported by Zeba Rizvi