id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
19902	ChimeraX bug report submission	zrizvi@…		"{{{
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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    ""path"" : ""\/usr\/lib\/system\/libdispatch.dylib"",
    ""name"" : ""libdispatch.dylib""
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    ""base"" : 6835560448,
    ""CFBundleShortVersionString"" : ""6.9"",
    ""CFBundleIdentifier"" : ""com.apple.CoreFoundation"",
    ""size"" : 5500928,
    ""uuid"" : ""8d45baee-6cc0-3b89-93fd-ea1c8e15c6d7"",
    ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"",
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    ""size"" : 3174368,
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    ""path"" : ""\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox"",
    ""name"" : ""HIToolbox""
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    ""source"" : ""P"",
    ""arch"" : ""arm64e"",
    ""base"" : 6831276032,
    ""size"" : 636280,
    ""uuid"" : ""3247e185-ced2-36ff-9e29-47a77c23e004"",
    ""path"" : ""\/usr\/lib\/dyld"",
    ""name"" : ""dyld""
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    ""source"" : ""A"",
    ""base"" : 0,
    ""uuid"" : ""00000000-0000-0000-0000-000000000000""
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    ""source"" : ""P"",
    ""arch"" : ""arm64e"",
    ""base"" : 6858567680,
    ""CFBundleShortVersionString"" : ""6.9"",
    ""CFBundleIdentifier"" : ""com.apple.Foundation"",
    ""size"" : 14587296,
    ""uuid"" : ""b9a92060-f21e-3ecf-9ded-94a65c68a6f4"",
    ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"",
    ""name"" : ""Foundation"",
    ""CFBundleVersion"" : ""3603""
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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
}}}
"	defect	new	normal		Unassigned