![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 days ago
Closed 27 hours ago
#20321 closed defect (duplicate)
Crash in QDockWidget::event() in Qt 6.9.2
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Web Services | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-26.4.1-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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"uptime" : 63000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,9",
"coalitionID" : 14982,
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"build" : "25E253",
"releaseType" : "User"
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"captureTime" : "2026-05-13 12:40:39.3996 -0500",
"codeSigningMonitor" : 2,
"incident" : "A6424E67-E3F1-4BF1-9DD3-2A95CF593EE8",
"pid" : 61469,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-05-13 12:32:51.5805 -0500",
"procStartAbsTime" : 1503311979531,
"procExitAbsTime" : 1514538818769,
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"procPath" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
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"parentPid" : 1,
"coalitionName" : "com.anthropic.claudefordesktop",
"crashReporterKey" : "5B537A52-51FC-54EC-2D23-7F9F50A625CF",
"appleIntelligenceStatus" : {"reasons":["notOptedIn","assetIsNotReady"],"state":"unavailable"},
"developerMode" : 1,
"responsiblePid" : 39516,
"responsibleProc" : "Python",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 1049ac000-1049b0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":61469},
"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4372217848
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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"uuid" : "f660af98-8bcc-35ff-a0a7-91590a2716eb",
"path" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_csv.cpython-311-darwin.so",
"name" : "_csv.cpython-311-darwin.so"
},
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"base" : 5574098944,
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"uuid" : "0d5e2b04-5266-3fcf-8917-51cab65a30b4",
"path" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGL.abi3.so",
"name" : "QtOpenGL.abi3.so"
},
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"path" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so",
"name" : "QtOpenGLWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5509480448,
"size" : 49152,
"uuid" : "bdbfbc59-c41d-3a69-8112-739716f2e836",
"path" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGLWidgets.framework\/Versions\/A\/QtOpenGLWidgets",
"name" : "QtOpenGLWidgets"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5512069120,
"size" : 81920,
"uuid" : "d92182fe-4f0b-3c92-8bb7-0b79cd82503a",
"path" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
"name" : "_ribbons.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5511905280,
"size" : 16384,
"uuid" : "1cc9ad85-9303-310d-acec-456c2181bee3",
"path" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
"name" : "_graphics.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5551702016,
"size" : 409600,
"uuid" : "3f1c3540-f7eb-3a3d-860e-c55452ccf717",
"path" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
"name" : "mmcif.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5613699072,
"size" : 376832,
"uuid" : "5d18d096-20ff-384b-84fb-bd6d8f5aaf40",
"path" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
"name" : "_mmcif.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
"base" : 5611749376,
"size" : 180224,
"uuid" : "8e2ee74d-d576-3b31-9afa-bcb515675310",
"path" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
"name" : "_pdbio.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
"base" : 5624512512,
"size" : 3768320,
"uuid" : "06082bf4-58c8-3f16-9f71-841cf9880fbe",
"path" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
"name" : "etree.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5542723584,
"size" : 131072,
"uuid" : "63b5bd02-9626-3588-a39c-88d4f882312b",
"path" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
"name" : "_elementpath.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6582710272,
"size" : 250512,
"uuid" : "51565b39-f595-3e96-a217-fef29815057a",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6582964224,
"size" : 52028,
"uuid" : "e7a73008-0c09-31e3-9dd9-0c61652f0e85",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6581477376,
"size" : 528120,
"uuid" : "66ebd321-6899-3863-ba24-5cfc3076a0cb",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6583017472,
"size" : 35060,
"uuid" : "d93ec420-f465-3a3a-916d-a04af9b023eb",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
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"arch" : "arm64e",
"base" : 6583250944,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5626976,
"uuid" : "04941709-2330-3bf8-9213-6d33964db448",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "4424.1.402"
},
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"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3125344,
"uuid" : "bcb81496-c81f-3d3e-a617-ccca047989e0",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
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"CFBundleShortVersionString" : "6.9",
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"size" : 24259264,
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"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2685.50.120"
},
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"name" : "dyld"
},
{
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"uuid" : "00000000-0000-0000-0000-000000000000"
},
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"sharedCache" : {
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},
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "a05a390aa82a7db582d69a66b4cff51870e02139",
"roots_installed" : 0,
"bug_type" : "309",
"trmStatus" : 1,
"trialInfo" : {
"rollouts" : [
{
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"factorPackIds" : [
],
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{
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}
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/pdamke/Desktop/Chimera Sessions/05-13-2028/AcCAST_for_R35.cxs"
Opened Full_J2530_resampled_sharp.mrc as #1, grid size 512,512,512, pixel
1.65, shown at level 0.119, step 1, values float32
Opened Full_J2530_resampled_sharp.mrc gaussian as #4, grid size 512,512,512,
pixel 1.65, shown at level 0.0735, step 1, values float32
Log from Mon May 4 17:36:01 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/ekello73/Desktop/AcCAST_model_grant_app
> copy/04_Full_map_withSTC_noDNA.cxs"
Opened Full_J2530_resampled_sharp.mrc as #1, grid size 512,512,512, pixel
1.65, shown at level 0.135, step 1, values float32
Log from Mon May 4 16:44:14 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/tpottang/Desktop/grant_model/Full_map_withSTC_noDNA.cxs
Opened 00_new_full_P59_J2530_resamples_sharp.mrc as #1, grid size 512,512,512,
pixel 1.65, shown at level 0.135, step 1, values float32
Log from Mon May 4 16:32:32 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/tpottang/Desktop/grant_model/Full_map_no_STC.cxs
Opened TightTarget_285A_J2871_sharp.mrc as #2, grid size 256,256,256, pixel
1.3, shown at level 0.0494, step 1, values float32
Opened 285A_B40_J2870_sharp.mrc as #3, grid size 256,256,256, pixel 1.3, shown
at level 0.132, step 1, values float32
Opened 00_new_full_P59_J2530_resamples_sharp.mrc as #6, grid size 512,512,512,
pixel 1.65, shown at level 0.135, step 1, values float32
Log from Mon May 4 16:03:19 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/tpottang/Desktop/grant_model/C06_S2_AcCAST_recruitment_004.pdb
Chain information for C06_S2_AcCAST_recruitment_004.pdb #1
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
A | No description available
B | No description available
C | No description available
D E F G H | No description available
> open /Users/tpottang/Desktop/grant_model/TightTarget_285A_J2871_sharp.mrc
Opened TightTarget_285A_J2871_sharp.mrc as #2, grid size 256,256,256, pixel
1.3, shown at level 8.48e-05, step 1, values float32
> lighting soft
> open /Users/tpottang/Desktop/grant_model/285A_B40_J2870_sharp.mrc
Opened 285A_B40_J2870_sharp.mrc as #3, grid size 256,256,256, pixel 1.3, shown
at level 0.0737, step 1, values float32
> volume #3 level 0.1187
> volume #2 level 0.00969
> hide
> show cartoons
> lighting soft
> lighting shadows true intensity 0.5
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> set bgColor white
> color #3 grey models
> color #3 #80808089 models
> color #3 #80808080 models
Called attribute on invalid object: 2147487593
[Repeated 21 time(s)]
> color #2 #b3b3b3ff models
> color #2 grey models
> color #2 #8080807f models
> open /Users/tpottang/Downloads/AcCAST_PD.pdb
Summary of feedback from opening /Users/tpottang/Downloads/AcCAST_PD.pdb
---
warnings | End residue of secondary structure not found: HELIX 1 1 GLU A 14 MET A 24 1 11
Start residue of secondary structure not found: HELIX 2 2 THR A 29 GLY A 40 1
12
Start residue of secondary structure not found: HELIX 3 3 ALA A 56 ASN A 64 1
9
Start residue of secondary structure not found: HELIX 4 4 GLY A 77 ALA A 83 1
7
Start residue of secondary structure not found: HELIX 5 5 ILE A 84 LEU A 86 1
3
Start residue of secondary structure not found: HELIX 6 6 VAL A 87 TYR A 91 1
5
1 messages similar to the above omitted
End residue of secondary structure not found: HELIX 8 8 ARG A 100 GLU A 106 1
7
Start residue of secondary structure not found: HELIX 9 9 GLY A 107 CYS A 109
1 3
Start residue of secondary structure not found: HELIX 10 10 ASP A 118 GLU A
120 1 3
Start residue of secondary structure not found: HELIX 11 11 LEU A 121 SER A
125 1 5
Start residue of secondary structure not found: HELIX 12 12 GLU A 130 ASN A
134 1 5
Start residue of secondary structure not found: HELIX 13 13 LEU A 139 PHE A
143 1 5
1 messages similar to the above omitted
End residue of secondary structure not found: HELIX 15 15 GLY A 202 GLY A 205
1 4
Start residue of secondary structure not found: HELIX 16 16 GLY A 222 ALA A
232 1 11
Start residue of secondary structure not found: HELIX 17 17 TRP A 250 GLU A
255 1 6
Start residue of secondary structure not found: HELIX 18 18 ILE A 256 THR A
258 1 3
Start residue of secondary structure not found: HELIX 19 19 GLU A 267 LEU A
275 1 9
Start residue of secondary structure not found: HELIX 20 20 ASN A 291 ASP A
293 1 3
End residue of secondary structure not found: HELIX 21 21 LEU A 325 ASN A 340
1 16
Start residue of secondary structure not found: HELIX 22 22 HIS A 368 VAL A
371 1 4
Start residue of secondary structure not found: HELIX 23 23 THR A 382 MET A
384 1 3
Start residue of secondary structure not found: HELIX 24 24 THR A 387 LYS A
407 1 21
Start residue of secondary structure not found: HELIX 25 25 GLN A 419 LEU A
429 1 11
Start residue of secondary structure not found: HELIX 26 26 VAL A 480 LEU A
484 1 5
134 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 GLU A 14 MET A 24 1 11
Start residue of secondary structure not found: HELIX 2 2 THR A 29 GLY A 40 1
12
Start residue of secondary structure not found: HELIX 3 3 ALA A 56 ASN A 64 1
9
Start residue of secondary structure not found: HELIX 4 4 GLY A 77 ALA A 83 1
7
Start residue of secondary structure not found: HELIX 5 5 ILE A 84 LEU A 86 1
3
Start residue of secondary structure not found: HELIX 6 6 VAL A 87 TYR A 91 1
5
1 messages similar to the above omitted
End residue of secondary structure not found: HELIX 8 8 ARG A 100 GLU A 106 1
7
Start residue of secondary structure not found: HELIX 9 9 GLY A 107 CYS A 109
1 3
Start residue of secondary structure not found: HELIX 10 10 ASP A 118 GLU A
120 1 3
Start residue of secondary structure not found: HELIX 11 11 LEU A 121 SER A
125 1 5
Start residue of secondary structure not found: HELIX 12 12 GLU A 130 ASN A
134 1 5
Start residue of secondary structure not found: HELIX 13 13 LEU A 139 PHE A
143 1 5
1 messages similar to the above omitted
End residue of secondary structure not found: HELIX 15 15 GLY A 202 GLY A 205
1 4
Start residue of secondary structure not found: HELIX 16 16 GLY A 222 ALA A
232 1 11
Start residue of secondary structure not found: HELIX 17 17 TRP A 250 GLU A
255 1 6
Start residue of secondary structure not found: HELIX 18 18 ILE A 256 THR A
258 1 3
Start residue of secondary structure not found: HELIX 19 19 GLU A 267 LEU A
275 1 9
Start residue of secondary structure not found: HELIX 20 20 ASN A 291 ASP A
293 1 3
End residue of secondary structure not found: HELIX 21 21 LEU A 325 ASN A 340
1 16
Start residue of secondary structure not found: HELIX 22 22 HIS A 368 VAL A
371 1 4
Start residue of secondary structure not found: HELIX 23 23 THR A 382 MET A
384 1 3
Start residue of secondary structure not found: HELIX 24 24 THR A 387 LYS A
407 1 21
Start residue of secondary structure not found: HELIX 25 25 GLN A 419 LEU A
429 1 11
Start residue of secondary structure not found: HELIX 26 26 VAL A 480 LEU A
484 1 5
134 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 GLU A 14 MET A 24 1 11
Start residue of secondary structure not found: HELIX 2 2 THR A 29 GLY A 40 1
12
Start residue of secondary structure not found: HELIX 3 3 ALA A 56 ASN A 64 1
9
Start residue of secondary structure not found: HELIX 4 4 GLY A 77 ALA A 83 1
7
Start residue of secondary structure not found: HELIX 5 5 ILE A 84 LEU A 86 1
3
Start residue of secondary structure not found: HELIX 6 6 VAL A 87 TYR A 91 1
5
1 messages similar to the above omitted
End residue of secondary structure not found: HELIX 8 8 ARG A 100 GLU A 106 1
7
Start residue of secondary structure not found: HELIX 9 9 GLY A 107 CYS A 109
1 3
Start residue of secondary structure not found: HELIX 10 10 ASP A 118 GLU A
120 1 3
Start residue of secondary structure not found: HELIX 11 11 LEU A 121 SER A
125 1 5
Start residue of secondary structure not found: HELIX 12 12 GLU A 130 ASN A
134 1 5
Start residue of secondary structure not found: HELIX 13 13 LEU A 139 PHE A
143 1 5
1 messages similar to the above omitted
End residue of secondary structure not found: HELIX 15 15 GLY A 202 GLY A 205
1 4
Start residue of secondary structure not found: HELIX 16 16 GLY A 222 ALA A
232 1 11
Start residue of secondary structure not found: HELIX 17 17 TRP A 250 GLU A
255 1 6
Start residue of secondary structure not found: HELIX 18 18 ILE A 256 THR A
258 1 3
Start residue of secondary structure not found: HELIX 19 19 GLU A 267 LEU A
275 1 9
Start residue of secondary structure not found: HELIX 20 20 ASN A 291 ASP A
293 1 3
End residue of secondary structure not found: HELIX 21 21 LEU A 325 ASN A 340
1 16
Start residue of secondary structure not found: HELIX 22 22 HIS A 368 VAL A
371 1 4
Start residue of secondary structure not found: HELIX 23 23 THR A 382 MET A
384 1 3
Start residue of secondary structure not found: HELIX 24 24 THR A 387 LYS A
407 1 21
Start residue of secondary structure not found: HELIX 25 25 GLN A 419 LEU A
429 1 11
Start residue of secondary structure not found: HELIX 26 26 VAL A 480 LEU A
484 1 5
134 messages similar to the above omitted
End residue of secondary structure not found: HELIX 1 1 GLU A 14 MET A 24 1 11
Start residue of secondary structure not found: HELIX 2 2 THR A 29 GLY A 40 1
12
Start residue of secondary structure not found: HELIX 3 3 ALA A 56 ASN A 64 1
9
Start residue of secondary structure not found: HELIX 4 4 GLY A 77 ALA A 83 1
7
Start residue of secondary structure not found: HELIX 5 5 ILE A 84 LEU A 86 1
3
Start residue of secondary structure not found: HELIX 6 6 VAL A 87 TYR A 91 1
5
1 messages similar to the above omitted
End residue of secondary structure not found: HELIX 8 8 ARG A 100 GLU A 106 1
7
Start residue of secondary structure not found: HELIX 9 9 GLY A 107 CYS A 109
1 3
Start residue of secondary structure not found: HELIX 10 10 ASP A 118 GLU A
120 1 3
Start residue of secondary structure not found: HELIX 11 11 LEU A 121 SER A
125 1 5
Start residue of secondary structure not found: HELIX 12 12 GLU A 130 ASN A
134 1 5
Start residue of secondary structure not found: HELIX 13 13 LEU A 139 PHE A
143 1 5
1 messages similar to the above omitted
End residue of secondary structure not found: HELIX 15 15 GLY A 202 GLY A 205
1 4
Start residue of secondary structure not found: HELIX 16 16 GLY A 222 ALA A
232 1 11
Start residue of secondary structure not found: HELIX 17 17 TRP A 250 GLU A
255 1 6
Start residue of secondary structure not found: HELIX 18 18 ILE A 256 THR A
258 1 3
Start residue of secondary structure not found: HELIX 19 19 GLU A 267 LEU A
275 1 9
Start residue of secondary structure not found: HELIX 20 20 ASN A 291 ASP A
293 1 3
End residue of secondary structure not found: HELIX 21 21 LEU A 325 ASN A 340
1 16
Start residue of secondary structure not found: HELIX 22 22 HIS A 368 VAL A
371 1 4
Start residue of secondary structure not found: HELIX 23 23 THR A 382 MET A
384 1 3
Start residue of secondary structure not found: HELIX 24 24 THR A 387 LYS A
407 1 21
Start residue of secondary structure not found: HELIX 25 25 GLN A 419 LEU A
429 1 11
Start residue of secondary structure not found: HELIX 26 26 VAL A 480 LEU A
484 1 5
134 messages similar to the above omitted
Chain information for AcCAST_PD.pdb
---
Chain | Description
4.1/1 | No description available
4.1/2 | No description available
4.1/3 | No description available
4.1/A | No description available
4.2/A 4.3/A 4.4/A 4.5/A | No description available
4.1/B | No description available
4.1/C | No description available
4.1/D 4.1/E 4.1/F 4.1/G 4.1/H | No description available
Computing secondary structure
[Repeated 3 time(s)]
> ui tool show Matchmaker
Called attribute on invalid object: 2147489647
[Repeated 21 time(s)]
Called attribute on invalid object: 2147491725
[Repeated 21 time(s)]
> hide #4.2 models
> hide #4.3 models
> hide #4.4 models
Called attribute on invalid object: 2147494640
[Repeated 21 time(s)]
> hide #4.5 models
> hide #!4.1 models
> show #!4.1 models
> chain info #4.1
Unknown command: chain info #4.1
> info chains #4.1
chain id #4.1/2 chain_id 2
chain id #4.1/3 chain_id 3
chain id #4.1/A chain_id A
chain id #4.1/B chain_id B
chain id #4.1/C chain_id C
chain id #4.1/D chain_id D
chain id #4.1/E chain_id E
chain id #4.1/F chain_id F
chain id #4.1/G chain_id G
chain id #4.1/H chain_id H
chain id #4.1/1 chain_id 1
> show #4.2 models
> show #4.3 models
> show #4.4 models
Called attribute on invalid object: 2147503925
[Repeated 21 time(s)]
> show #4.5 models
> hide #4.5 models
> hide #4.4 models
> hide #4.3 models
> hide #4.2 models
> hide #!4.1 models
> hide #!4 models
Called attribute on invalid object: 2147512941
[Repeated 21 time(s)]
> close #4
> color /1 #decb6a
> color /2 #6f6ade
> color /3 #de726a
> color /A #464561
> color /B #3ae080
> color /C #8a706e
> color /D,F,H #df68ff
> color /E,G,I #ab58b9
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> combine #1/E
> color #4 #9c9c9cff
Called attribute on invalid object: 2147523743
[Repeated 21 time(s)]
> undo
> hide #!1 models
> show #!1 models
> color #4 #9c9c9cff
> undo
> hide #!1 models
> hide #!4 models
> show #!4 models
Called attribute on invalid object: 2147535116
[Repeated 21 time(s)]
> select #4
25081 atoms, 26244 bonds, 2 pseudobonds, 2563 residues, 2 models selected
> ~select #4/F
22960 atoms, 24091 bonds, 2 pseudobonds, 2299 residues, 2 models selected
> delete sel
> show #!1 models
> hide #!1 models
> show #!1 models
> combine #1/E
> select #5
25081 atoms, 26244 bonds, 2 pseudobonds, 2563 residues, 2 models selected
> ~select #5/E
22960 atoms, 24091 bonds, 2 pseudobonds, 2299 residues, 2 models selected
> delete sel
> hide #!1 models
Called attribute on invalid object: 2147551162
[Repeated 21 time(s)]
> rename #4 TnsC_F
Called attribute on invalid object: 2147553932
[Repeated 21 time(s)]
> ~select #5/E
Nothing selected
> rename #5 TnsC_E
> color #5 #ab58b8ff
> color #5 #9f58b8ff
> color #5 #9f68b8ff
> color #5 #9f68d2ff
> show #!1 models
Called attribute on invalid object: 2147565288
[Repeated 21 time(s)]
> hide #!4 models
> hide #!5 models
> color /1 #decb6a
> color /2 #6f6ade
> color /3 #de726a
> color /A #464561
> color /B #3ae080
> color /C #8a706e
> color /D,F,H #df68ff
> color /E,G,I #9f68d2
> show #!2 models
> volume #2 level 0.0385
Called attribute on invalid object: 2147572757
[Repeated 21 time(s)]
> hide #!2 models
> show #!3 models
> volume #3 level 0.1861
> ui tool show "Color Zone"
> color zone #3 near #1 distance 7.78
> volume #2 level 0.04941
> hide #!2 models
> volume #3 level 0.1765
> hide #!1 models
> volume #3 level 0.1319
Called attribute on invalid object: 2147589196
[Repeated 21 time(s)]
> save /Users/tpottang/Desktop/grant_model/Recruitment_map_sharp.cxs
> hide #!3 models
> show #!2 models
> show #!1 models
> color zone #2 near #1 distance 7.78
Called attribute on invalid object: 2147599158
[Repeated 21 time(s)]
> save /Users/tpottang/Desktop/grant_model/Recruitment_map_EMhancer.cxs
> open
> /Users/tpottang/Desktop/Coot_Session/Coot_005/Session_2/00_new_full_P59_J2530_resamples_sharp.mrc
Opened 00_new_full_P59_J2530_resamples_sharp.mrc as #6, grid size 512,512,512,
pixel 1.65, shown at level 0.0222, step 2, values float32
> color #6 #edededff models
> color #6 grey models
> color #6 #8080807d models
> color #6 #7f7f7f7d models
Called attribute on invalid object: 2147610054
[Repeated 21 time(s)]
> volume #6 step 1
> volume #6 step 2
> hide #!2 models
> volume #6 level 0.03755
> volume #6 step 1
> volume #6 level 0.06724
> ui tool show "Fit in Map"
> fitmap #6 inMap #3
Fit map 00_new_full_P59_J2530_resamples_sharp.mrc in map
285A_B40_J2870_sharp.mrc using 218511 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of 00_new_full_P59_J2530_resamples_sharp.mrc (#6) relative to
285A_B40_J2870_sharp.mrc (#3) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
> select add #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,-105.46,0,1,0,33.977,0,0,1,-242.2
> view matrix models #6,1,0,0,-256.26,0,1,0,-219.67,0,0,1,-241.72
> view matrix models #6,1,0,0,-239.48,0,1,0,-252.35,0,0,1,-231.84
> view matrix models #6,1,0,0,-244.97,0,1,0,-247.07,0,0,1,-244.65
> view matrix models
> #6,0.13485,-0.98857,-0.067425,567.09,0.96307,0.11476,0.24356,-472.21,-0.23304,-0.09778,0.96754,-83.516
> view matrix models
> #6,0.13485,-0.98857,-0.067425,592.22,0.96307,0.11476,0.24356,-427.62,-0.23304,-0.09778,0.96754,-77.569
> view matrix models
> #6,0.13485,-0.98857,-0.067425,549.04,0.96307,0.11476,0.24356,-395.39,-0.23304,-0.09778,0.96754,-83.343
> fitmap #6 inMap #3
Fit map 00_new_full_P59_J2530_resamples_sharp.mrc in map
285A_B40_J2870_sharp.mrc using 218511 points
correlation = 0.3963, correlation about mean = 0.08938, overlap = 1277
steps = 864, shift = 13.9, angle = 21.3 degrees
Position of 00_new_full_P59_J2530_resamples_sharp.mrc (#6) relative to
285A_B40_J2870_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.23359617 -0.97158680 -0.03810405 689.79091582
0.94439979 -0.23603679 0.22890102 -222.63510864
-0.23139117 0.01748494 0.97270366 -140.64443760
Axis -0.10913026 0.09977232 0.98900762
Axis point 415.20437418 156.21604391 0.00000000
Rotation angle (degrees) 104.38667687
Shift along axis -236.58830450
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> view matrix models
> #6,-0.2336,-0.97159,-0.038104,693.43,0.9444,-0.23604,0.2289,-222.88,-0.23139,0.017485,0.9727,-136.61
> view matrix models
> #6,-0.2336,-0.97159,-0.038104,802.76,0.9444,-0.23604,0.2289,-251.1,-0.23139,0.017485,0.9727,-61.824
> volume #6 level 0.1351
> view matrix models
> #6,-0.2336,-0.97159,-0.038104,805.06,0.9444,-0.23604,0.2289,-253.75,-0.23139,0.017485,0.9727,-64.791
> view matrix models
> #6,0.10892,0.98958,0.094129,-212.64,-0.95191,0.076552,0.29665,383.06,0.28636,-0.12191,0.95033,-214.48
> view matrix models
> #6,0.10892,0.98958,0.094129,-209.61,-0.95191,0.076552,0.29665,355.76,0.28636,-0.12191,0.95033,-263.69
> view matrix models
> #6,0.10892,0.98958,0.094129,-260.91,-0.95191,0.076552,0.29665,348.1,0.28636,-0.12191,0.95033,-283.66
> view matrix models
> #6,0.10892,0.98958,0.094129,-279.85,-0.95191,0.076552,0.29665,385.97,0.28636,-0.12191,0.95033,-254.15
> view matrix models
> #6,0.10892,0.98958,0.094129,-303.81,-0.95191,0.076552,0.29665,385.3,0.28636,-0.12191,0.95033,-275.96
> view matrix models
> #6,-0.20776,0.9519,0.22521,-214.42,-0.91801,-0.26925,0.29116,517.03,0.33779,-0.14625,0.92979,-278.17
> view matrix models
> #6,-0.20776,0.9519,0.22521,-227.67,-0.91801,-0.26925,0.29116,555.69,0.33779,-0.14625,0.92979,-287.86
> view matrix models
> #6,0.87998,0.46224,-0.10942,-330.16,-0.44132,0.88078,0.17166,-67.794,0.17573,-0.10277,0.97906,-260.1
> view matrix models
> #6,0.87998,0.46224,-0.10942,-330.25,-0.44132,0.88078,0.17166,-81.371,0.17573,-0.10277,0.97906,-259.34
> view matrix models
> #6,0.87998,0.46224,-0.10942,-342.78,-0.44132,0.88078,0.17166,-92.159,0.17573,-0.10277,0.97906,-256.66
> fitmap #6 inMap #3
Fit map 00_new_full_P59_J2530_resamples_sharp.mrc in map
285A_B40_J2870_sharp.mrc using 90411 points
correlation = 0.6254, correlation about mean = 0.2904, overlap = 2025
steps = 252, shift = 22, angle = 13.9 degrees
Position of 00_new_full_P59_J2530_resamples_sharp.mrc (#6) relative to
285A_B40_J2870_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.90384918 0.30897439 -0.29595858 -226.36256515
-0.28396823 0.95062447 0.12520050 -163.18871223
0.32002922 -0.02911954 0.94696006 -341.01242842
Axis -0.17762163 -0.70899903 -0.68247413
Axis point 141.07727232 0.00000000 -577.43365398
Rotation angle (degrees) 25.74754494
Shift along axis 388.63968611
> hide #!2 models
> select subtract #6
Nothing selected
> show #!1 models
> fitmap #6 inMap #3
Fit map 00_new_full_P59_J2530_resamples_sharp.mrc in map
285A_B40_J2870_sharp.mrc using 90411 points
correlation = 0.6254, correlation about mean = 0.2905, overlap = 2025
steps = 80, shift = 0.0137, angle = 0.00252 degrees
Position of 00_new_full_P59_J2530_resamples_sharp.mrc (#6) relative to
285A_B40_J2870_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.90384022 0.30896472 -0.29599606 -226.35067110
-0.28396400 0.95062852 0.12517933 -163.18151047
0.32005829 -0.02908989 0.94695115 -341.02759778
Axis -0.17755727 -0.70905222 -0.68243561
Axis point 141.17371119 0.00000000 -577.44999943
Rotation angle (degrees) 25.74845678
Shift along axis 388.62379806
> color zone #6 near #1 distance 9.88
> color zone #6 near #1 distance 9
[Repeated 2 time(s)]
> color zone #6 near #1 distance 5
[Repeated 1 time(s)]
> undo
[Repeated 5 time(s)]
> color zone #6 near #1 distance 5
> color zone #6 near #1 distance 6
> save /Users/tpottang/Desktop/grant_model/Full_map_no_STC.cxs
——— End of log from Mon May 4 16:03:19 2026 ———
> view name session-start
opened ChimeraX session
> open /Users/tpottang/Desktop/grant_model/AcCAST_no_STC_DNA.pdb
Chain information for AcCAST_no_STC_DNA.pdb #7
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
A | No description available
B | No description available
C | No description available
D E F G H | No description available
J K L M | No description available
> hide
> show cartoons
> ui tool show Matchmaker
Called attribute on invalid object: 2147487447
[Repeated 21 time(s)]
> matchmaker #!7 to #1
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 C06_S2_AcCAST_recruitment_004.pdb, chain A (#1) with
AcCAST_no_STC_DNA.pdb, chain A (#7), sequence alignment score = 3300.7
RMSD between 642 pruned atom pairs is 0.000 angstroms; (across all 642 pairs:
0.000)
Called attribute on invalid object: 2147489148
[Repeated 21 time(s)]
Called attribute on invalid object: 2147489087
[Repeated 21 time(s)]
Called attribute on invalid object: 2147490786
[Repeated 21 time(s)]
> save /Users/tpottang/Desktop/grant_model/AcCAST_no_STC_DNA.pdb models #7
> relModel #1
> hide #!1 models
> hide #!6 models
> show #!1 models
> color /1 #decb6a
> color /2 #6f6ade
> color /3 #de726a
> color /A #464561
> color /B #3ae080
> color /C #8a706e
> color /D,F,H #df68ff
> color /E,G,I #9f68d2
> hide #!1 models
> color /1 #decb6a
> color /2 #6f6ade
> color /3 #de726a
> color /A #464561
> color /B #3ae080
> color /C #8a706e
> color /D,F,H #df68ff
> color /E,G,I #9f68d2
> color /J,L #4ac4d8
> color /K,M #2d8a9e
> color /1 #decb6a
> color /2 #6f6ade
> color /3 #de726a
> color /A #464561
> color /B #3ae080
> color /C #8a706e
> color /D,F,H #df68ff
> color /E,G,I #9f68d2
> color /J,K #5dd4c4
> color /L,M #3a9b8e
> color /1 #decb6a
> color /2 #6f6ade
> color /3 #de726a
> color /A #464561
> color /B #3ae080
> color /C #8a706e
> color /D,F,H #df68ff
> color /E,G,I #9f68d2
> color /J,M #5dd4c4
> color /K,L #3a9b8e
> color /J,M #3ad6d6
> color /K,L #2a9b9b
> color /J,M #5dd4c4
> color /K,L #3a9b8e
> show #!2 models
Called attribute on invalid object: 2147503452
[Repeated 21 time(s)]
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> ui tool show "Color Zone"
> color zone #6 near #7 distance 1.65
[Repeated 1 time(s)]
> color zone #6 near #7 distance 15.88
> color zone #6 near #7 distance 10
> color zone #6 near #7 distance 9
> color zone #6 near #7 distance 8
> hide #!7 models
Called attribute on invalid object: 2147520980
[Repeated 21 time(s)]
> close #1-5
> rename #6 #1
No name or id option specified for renaming
> rename #6 id #1
> rename #7 id #2
Called attribute on invalid object: 2147527433
[Repeated 21 time(s)]
> save /Users/tpottang/Desktop/grant_model/Full_map_withSTC_noDNA.cxs
——— End of log from Mon May 4 16:32:32 2026 ———
> view name session-start
opened ChimeraX session
> rename #1 Full_J2530_resampled_sharp.mrc
Called attribute on invalid object: 2147485600
[Repeated 21 time(s)]
Called attribute on invalid object: 2147486384
[Repeated 21 time(s)]
> save /Users/tpottang/Desktop/grant_model/Full_map_withSTC_noDNA.cxs
> includeMaps true
——— End of log from Mon May 4 16:44:14 2026 ———
> view name session-start
opened ChimeraX session
> show #!2 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.1166
> volume style surface
> transparency 0
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> open 7SVW
Summary of feedback from opening 7SVW fetched from pdb
---
note | Fetching compressed mmCIF 7svw from http://files.rcsb.org/download/7svw.cif
7svw title:
Strand-transfer complex of TnsB from ShCAST [more info...]
Chain information for 7svw #3
---
Chain | Description
1 4 | STC_LE_For
2 5 | STC_LE_Rev1
3 6 | STC_LE_Rev2
A B C D | TnsB
Non-standard residues in 7svw #3
---
MG — magnesium ion
> show cartoons
> hide cartoons
> hide atoms
> show cartoons
> matchmaker #3 to #2/K
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 AcCAST_no_STC_DNA.pdb, chain K (#2) with 7svw, chain B (#3),
sequence alignment score = 1042.1
RMSD between 206 pruned atom pairs is 1.035 angstroms; (across all 433 pairs:
15.651)
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.1191
> hide #!1 models
> show #!1 models
> ui tool show "Map Filter"
> volume gaussian #1 sDev 1.74
Opened Full_J2530_resampled_sharp.mrc gaussian as #4, grid size 512,512,512,
pixel 1.65, shown at step 1, values float32
> volume #4 level 0.06925
> volume #4 level 0.07347
> lighting soft
> hide #!3 models
> hide #!4 models
> color #2/1 #ff6a6a
> color #2/2 #fdff9a
> color #2/3 #fdf09a
> color #2/A #ffadff
> color #2/B #98bfff
> color #2/C #88f5ff
> color #2/D-I #a9ff95
> color #2/J-M #ffadff
> color #2/J-M #a294ff
> color zone #4 near #2 distance 10
> show #!4 models
> show #!3 models
> hide #!2 models
> hide #!4 models
> color #3/2 #fdff9a
> color #3/5 #fdff9a
> color #3/4 #fdf09a
> color #3/1 #fdf09a
> color #3/A-D #a294ff
> color zone #4 near #2,3 distance 4
> show #!4 models
> color zone #4 near #2,3 distance 8
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!3 models
> hide #!4 models
> combine #2/H
> select add #5
39585 atoms, 41084 bonds, 2 pseudobonds, 4335 residues, 2 models selected
> select subtract #5
Nothing selected
> select add #5
39585 atoms, 41084 bonds, 2 pseudobonds, 4335 residues, 2 models selected
> select #5/H
2121 atoms, 2153 bonds, 264 residues, 1 model selected
> select ~sel & ##selected
37464 atoms, 38931 bonds, 2 pseudobonds, 4071 residues, 2 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> select add #5
2121 atoms, 2153 bonds, 264 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.80497,-0.53833,-0.24945,124.77,0.56963,0.81881,0.071159,-438.89,0.16595,-0.19938,0.96577,-218.24
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.80497,-0.53833,-0.24945,153.99,0.56963,0.81881,0.071159,-446.61,0.16595,-0.19938,0.96577,-196.92
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.14215,-0.98809,-0.058874,513.9,0.97572,0.14988,-0.15968,-246.25,0.16661,-0.034745,0.98541,-270.44
> view matrix models
> #5,0.263,-0.8878,-0.37769,571.13,0.9529,0.17774,0.24575,-433.31,-0.15105,-0.42453,0.89272,54.262
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.263,-0.8878,-0.37769,566.68,0.9529,0.17774,0.24575,-423.08,-0.15105,-0.42453,0.89272,52.811
> fitmap # 5inMap #4
Missing or invalid "atomsOrMap" argument: invalid atom specifier
> fitmap #5 inMap #4
Fit molecule copy of AcCAST_no_STC_DNA.pdb (#5) to map
Full_J2530_resampled_sharp.mrc gaussian (#4) using 2121 atoms
average map value = 0.0943, steps = 312
shifted from previous position = 22
rotated from previous position = 58.4 degrees
atoms outside contour = 601, contour level = 0.07347
Position of copy of AcCAST_no_STC_DNA.pdb (#5) relative to
Full_J2530_resampled_sharp.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.52065199 -0.74134327 0.42347568 304.13775764
0.59581209 0.67075407 0.44169778 -314.71906516
-0.61149771 0.02234110 0.79093073 341.81783214
Axis -0.24071502 0.59408530 0.76754084
Axis point 558.08074356 50.10809398 0.00000000
Rotation angle (degrees) 60.58259419
Shift along axis 2.17865005
> hide #!4 models
> show #!4 models
> hide #!4 models
> ui mousemode right "translate selected models"
> show #!4 models
> view matrix models
> #5,0.83567,-0.46943,0.28511,-143.93,0.342,0.85095,0.39865,-496.09,-0.42975,-0.23563,0.87166,89.846
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.62822,-0.7766,0.047163,169.85,0.65343,0.55955,0.50984,-560.83,-0.42233,-0.28947,0.85898,113.62
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.62822,-0.7766,0.047163,185.21,0.65343,0.55955,0.50984,-559.29,-0.42233,-0.28947,0.85898,124.57
> view matrix models
> #5,0.62822,-0.7766,0.047163,184.15,0.65343,0.55955,0.50984,-569.54,-0.42233,-0.28947,0.85898,127.1
> fitmap #5 inMap #4
Fit molecule copy of AcCAST_no_STC_DNA.pdb (#5) to map
Full_J2530_resampled_sharp.mrc gaussian (#4) using 2121 atoms
average map value = 0.0943, steps = 288
shifted from previous position = 25
rotated from previous position = 25.5 degrees
atoms outside contour = 602, contour level = 0.07347
Position of copy of AcCAST_no_STC_DNA.pdb (#5) relative to
Full_J2530_resampled_sharp.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.52060272 -0.74144609 0.42335623 304.24467679
0.59675690 0.67060979 0.44064011 -314.58471788
-0.61061772 0.02324232 0.79158435 340.80420377
Axis -0.23962629 0.59360003 0.76825662
Axis point 557.31409928 50.70201870 0.00000000
Rotation angle (degrees) 60.56746204
Shift along axis 2.18256441
> close #5
> combine #2/H
> hide #!4 models
> hide #!2 models
> select #5/G,H
4242 atoms, 4306 bonds, 528 residues, 1 model selected
> select ~sel & ##selected
35343 atoms, 36778 bonds, 2 pseudobonds, 3807 residues, 2 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> show #!4 models
> select add #5
4242 atoms, 4306 bonds, 528 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.79815,-0.58809,-0.13078,103.31,0.55674,0.63704,0.53312,-559,-0.23021,-0.49833,0.83587,120.15
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.79815,-0.58809,-0.13078,124.23,0.55674,0.63704,0.53312,-565.18,-0.23021,-0.49833,0.83587,138.43
> fitmap #5 inMap #4
Fit molecule copy of AcCAST_no_STC_DNA.pdb (#5) to map
Full_J2530_resampled_sharp.mrc gaussian (#4) using 4242 atoms
average map value = 0.0957, steps = 104
shifted from previous position = 6.87
rotated from previous position = 13.8 degrees
atoms outside contour = 1097, contour level = 0.07347
Position of copy of AcCAST_no_STC_DNA.pdb (#5) relative to
Full_J2530_resampled_sharp.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.50679091 -0.86206353 0.00307127 570.84070822
0.84127553 0.49534152 0.21654620 -240.02366360
-0.18819791 -0.10715987 0.97626754 143.74420728
Axis -0.18557475 0.10965111 0.97649303
Axis point 509.70536604 372.31004138 0.00000000
Rotation angle (degrees) 60.71198716
Shift along axis 8.11273404
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> color zone #4 near #2,3,5 distance 8
> color zone #4 near #2,3,5 distance 15
> color zone #4 near #2,3,5 distance 20
> color zone #4 near #2,3,5 distance 15
> color zone #4 near #2,3,5 distance 10
> color #4 #fdff9a
> color zone #4 near #2,3,5 distance 10
> hide #!5 models
> color zone #4 near #2,3,5 distance 11
> color zone #4 near #2,3,5 distance 12
> save /Users/ekello73/Desktop/AcCAST_integration_complex.png supersample 300
> save /Users/ekello73/Desktop/AcCAST_for_R35.cxs
——— End of log from Mon May 4 17:36:01 2026 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,9
Model Number: MPHH3LL/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 Performance and 4 Efficiency)
Memory: 16 GB
System Firmware Version: 18000.101.7
OS Loader Version: 18000.101.7
Software:
System Software Overview:
System Version: macOS 26.4.1 (25E253)
Kernel Version: Darwin 25.4.0
Time since boot: 4 days, 19 hours, 52 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
DELL U3423WE:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
Change History (2)
comment:1 by , 27 hours ago
| Component: | Unassigned → Web Services |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in QDockWidget::event() in Qt 6.9.2 |
comment:2 by , 27 hours ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Known Qt 6.9 crash dragging tool windows. Appears fixed in Qt 6.10.