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Opened 107 minutes ago
#19902 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
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,
"osVersion" : {
"train" : "macOS 15.6.1",
"build" : "24G90",
"releaseType" : "User"
},
"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",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"6EB36192-985F-52AF-B8E6-46C6ECBF748E","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E2796449-E3BF-8B60-EBDE-A5CD5F936DBB",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
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"wakeTime" : 14052,
"sleepWakeUUID" : "CCFCD64F-6A4C-46BD-9D26-F9B51F8E85A8",
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"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
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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
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