![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Closed 13 months ago
#16075 closed defect (can't reproduce)
QWebEngine crash
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
{"app_name":"ChimeraX","timestamp":"2024-10-06 15:05:04.00 +0200","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.6.1 (23G93)","roots_installed":0,"name":"ChimeraX","incident_id":"96E6D151-502B-46BF-9514-800199F96700"}
{
"uptime" : 42000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 2792,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2024-10-06 15:04:49.6633 +0200",
"codeSigningMonitor" : 0,
"incident" : "96E6D151-502B-46BF-9514-800199F96700",
"pid" : 37885,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-10-06 15:03:20.5024 +0200",
"procStartAbsTime" : 42278269094110,
"procExitAbsTime" : 42367424901091,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"93EBC951-EAE0-5D92-BB64-C33EFF66BE7C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B1A2D307-A826-85E8-6A12-ECEC2178B5E3",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 11041,
"bridgeVersion" : {"build":"21P6074","train":"8.6"},
"sleepWakeUUID" : "008B015C-2EE5-42B7-8D22-C8FC8631F1A3",
"sip" : "enabled",
"vmRegionInfo" : "0x3e800000449 is not in any region. Bytes after previous region: 4289105413194 Bytes before following region: 101258148969399\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n VM_ALLOCATE 15d554000-15d654000 [ 1024K] rw-\/rwx SM=PRV \n---> GAP OF 0x5ffea29ac000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x000003e800000449","rawCodes":[1,4294967297097],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000003e800000449"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"exc handler","byPid":37885},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x3e800000449 is not in any region. Bytes after previous region: 4289105413194 Bytes before following region: 101258148969399\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n VM_ALLOCATE 15d554000-15d654000 [ 1024K] rw-\/rwx SM=PRV \n---> GAP OF 0x5ffea29ac000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
"threads" : 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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/fcntl.cpython-311-darwin.so",
"name" : "fcntl.cpython-311-darwin.so"
},
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"size" : 32768,
"uuid" : "6333bf6e-f980-3714-b65f-a12997bfe10a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_struct.cpython-311-darwin.so",
"name" : "_struct.cpython-311-darwin.so"
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"uuid" : "dc4ae342-b3c4-3716-a530-b1568a67f912",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/binascii.cpython-311-darwin.so",
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"uuid" : "4e6494eb-704b-3e1a-9d97-751ef9b2d06a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_sha512.cpython-311-darwin.so",
"name" : "_sha512.cpython-311-darwin.so"
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"uuid" : "de8dfc82-ec28-378b-b945-07e7671a35b1",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_random.cpython-311-darwin.so",
"name" : "_random.cpython-311-darwin.so"
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"size" : 16384,
"uuid" : "cc52d89b-b174-3a9a-94ae-0c556ec7b21b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_bisect.cpython-311-darwin.so",
"name" : "_bisect.cpython-311-darwin.so"
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"uuid" : "0fa75f51-66bf-3a60-a393-65ceea03012e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_lzma.cpython-311-darwin.so",
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"uuid" : "4921b552-b90a-39c6-b791-14028366f5a0",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_bz2.cpython-311-darwin.so",
"name" : "_bz2.cpython-311-darwin.so"
},
{
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"uuid" : "6c0e3849-f845-3996-a69e-e956c62499ff",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/zlib.cpython-311-darwin.so",
"name" : "zlib.cpython-311-darwin.so"
},
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"uuid" : "52112d00-a676-3fba-b4d8-69e98fe5e2c3",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_typing.cpython-311-darwin.so",
"name" : "_typing.cpython-311-darwin.so"
},
{
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"size" : 65536,
"uuid" : "ce1cdda7-c310-3834-8656-4829f8b0fa2a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_datetime.cpython-311-darwin.so",
"name" : "_datetime.cpython-311-darwin.so"
},
{
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"uuid" : "c4d4107c-7508-3d61-88f1-4f1a33945090",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/math.cpython-311-darwin.so",
"name" : "math.cpython-311-darwin.so"
},
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"size" : 4030464,
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python",
"name" : "Python",
"CFBundleVersion" : "3.11.4"
},
{
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"size" : 16384,
"uuid" : "194a3167-3db5-3029-8d22-1d742b826bb9",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
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"uuid" : "4ea5bbf7-8ce1-37ab-916b-d14ffd7d2b4b",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703433441280,
"CFBundleShortVersionString" : "6.9",
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"size" : 4829181,
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"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "2602"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703612137472,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 2732020,
"uuid" : "2aa738bf-9f72-3227-8bba-7eae7b9f080b",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703490764800,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 21172216,
"uuid" : "d0e19a37-f677-32b5-b3d2-005e60b90f7f",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2487.70.105"
},
{
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"base" : 140703429300224,
"size" : 591904,
"uuid" : "18f658dd-20f3-324d-b7ac-8a9c60b574b3",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
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"name" : "libsystem_pthread.dylib"
},
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"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
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Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/interactionsite.cxs"
Log from Sun Oct 6 15:21:54 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/Mutant2_zoom.cxs"
Log from Sun Oct 6 13:09:19 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/Mutant5.cxs"
Log from Fri Oct 4 15:32:18 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/TOPview.cxs"
Log from Fri Oct 4 15:13:12 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/Top.cxs"
Log from Wed Sep 18 22:21:14 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 5.cxs"
Log from Wed Sep 18 22:00:52 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 2.cxs"
Log from Wed Sep 18 21:35:21 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/lks559/Desktop/CINP-c1orf109_refine_13-coot.pdb
Chain information for CINP-c1orf109_refine_13-coot.pdb #1
---
Chain | Description
A C | No description available
B D | No description available
> set bgColor white
> lighting soft
> color #1 #678ad7ff
> select /A:2-203
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> select /C:2-203
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> ui tool show "Unit Cell"
> ui tool show "Crystal Contacts"
> crystalcontacts #1
8 pairs of asymmetric units of CINP-c1orf109_refine_13-coot.pdb contact at
distance 3.0 A
Atoms MTRIX SMTRY Unit cell MTRIXref Copies
6 0 1 -1 1 -1 0 1
5 0 3 0 0 1 0 1
5 0 1 -1 1 0 0 1
4 0 3 -1 0 1 0 1
3 0 1 0 1 0 0 1
3 0 1 0 1 -1 0 1
1 0 0 1 0 0 0 1
1 0 0 -1 0 0 0 1
> select /D:17-212
14319 atoms, 14607 bonds, 1764 residues, 9 models selected
> select /C:2-203
14751 atoms, 15012 bonds, 1818 residues, 9 models selected
> select /D:17-212
14319 atoms, 14607 bonds, 1764 residues, 9 models selected
> select /C:2-203
14751 atoms, 15012 bonds, 1818 residues, 9 models selected
> select /D:17-212
14319 atoms, 14607 bonds, 1764 residues, 9 models selected
> select #2.1/D
1591 atoms, 1623 bonds, 196 residues, 1 model selected
> hide sel cartoons
> select #1/B#2.1/B#2.2/B#2.3/B#2.4/B#2.5/B#2.6/B#2.7/B#2.8/B
14319 atoms, 14607 bonds, 1764 residues, 9 models selected
> hide sel cartoons
> select #1/A#2.1/A#2.2/A#2.3/A#2.4/A#2.5/A#2.6/A#2.7/A#2.8/A
14751 atoms, 15012 bonds, 1818 residues, 9 models selected
> hide sel cartoons
> select #2.1/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> hide sel cartoons
> select #2.2/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> hide sel cartoons
> select #2.3/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> hide sel cartoons
> select #2.4/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> hide sel cartoons
> select #1/C#2.1/C#2.2/C#2.3/C#2.4/C#2.5/C#2.6/C#2.7/C#2.8/C
14751 atoms, 15012 bonds, 1818 residues, 9 models selected
> hide sel cartoons
> select #2.2/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> show sel cartoons
> select #1/D#2.1/D#2.2/D#2.3/D#2.4/D#2.5/D#2.6/D#2.7/D#2.8/D
14319 atoms, 14607 bonds, 1764 residues, 9 models selected
> hide sel cartoons
> select #2.2/D
1591 atoms, 1623 bonds, 196 residues, 1 model selected
> show sel cartoons
> select #1/C#2.1/C#2.2/C#2.3/C#2.4/C#2.5/C#2.6/C#2.7/C#2.8/C
14751 atoms, 15012 bonds, 1818 residues, 9 models selected
> show sel cartoons
> select #1/C#2.1/C#2.2/C#2.3/C#2.4/C#2.5/C#2.6/C#2.7/C#2.8/C
14751 atoms, 15012 bonds, 1818 residues, 9 models selected
> hide sel cartoons
> select #1/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> show sel cartoons
> select add #1
6460 atoms, 6582 bonds, 796 residues, 1 model selected
> select subtract #1
Nothing selected
> select #1/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> color sel dim gray
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/biological unit.cxs"
> color #2 #356abfff models
> select #2.2/D
1591 atoms, 1623 bonds, 196 residues, 1 model selected
> color sel orange
> select add #2
51680 atoms, 52656 bonds, 6368 residues, 9 models selected
> select subtract #2
Nothing selected
> select #1/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> color sel hot pink
> open /Users/lks559/Desktop/CINP-c1orf109_refine_13-coot.pdb
Chain information for CINP-c1orf109_refine_13-coot.pdb #3
---
Chain | Description
A C | No description available
B D | No description available
> select #3/B
1591 atoms, 1623 bonds, 196 residues, 1 model selected
> hide sel cartoons
> select #3/D
1591 atoms, 1623 bonds, 196 residues, 1 model selected
> color sel medium blue
> select #3/A
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> color sel lime
> select #3/D
1591 atoms, 1623 bonds, 196 residues, 1 model selected
> color midnight blue
> color sel #ffffffff
> color sel #011993ff
> color midnightblue blueselect #3/A
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #3/A
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> color sel #73fa79ff
> color sel #0096ffff
> color sel #0433ffff
> color sel #0096ffff
> select #1/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> color sel #73fa79ff
> color sel #00f900ff
> color sel #73fa79ff
> select #1/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> select #3/A
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> color sel #0096ffff
> color sel #0433ffff
> color sel #7a81ffff
> color sel #0096ffff
> color sel #0433ffff
> color sel #0096ffff
> color sel #0433ffff
> select #1/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> color sel #ff9300ff
> color sel #ff2600ff
> color sel #ff7e79ff
> color #3 #ff9300ff
> undo
> select #1/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> hide #3 models
> show #3 models
> hide #3 models
> color #3 #ff2600ff
> show #3 models
> color #3 #ff9300ff
> color #1 #ff9300ff
> select #3/A
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> color #1 #011993ff
> hide #3 models
> show #3 models
> hide #1 models
> show #1 models
> hide #3 models
> color #1 #ff9300ff
> select #3/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> hide #1#2.1-8 cartoons
> undo
> show #3 models
> hide #!2 models
> hide #1 models
> show #1 models
> show #!2 models
> hide #!2 models
> hide #1 models
> show #1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> color #2 #73fa79ff models
> color #2 #ffd479ff models
> color #2 #fffb00ff models
> color #2 #fffc79ff models
> color #2 #ffd479ff models
> hide #!2 models
> hide #1 models
> hide #3 models
> show #1 models
> hide #1 models
> show #3 models
> select #3/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> hide sel cartoons
> show #!2 models
> hide #!2 models
> show #1 models
> hide #1 models
> select #3/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> color sel #011993ff
[Repeated 2 time(s)]
> show #!2 models
> hide #!2 models
> show #1 models
> hide #1 models
> select #3/A
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> color sel #005493ff
> color sel #011993ff
> color sel #000000ff
> color sel #212121ff
> color sel #011993ff
> select #3/B
1591 atoms, 1623 bonds, 196 residues, 1 model selected
> show sel cartoons
> show #!2 models
> show #1 models
> color sel #0433ffff
> color sel #0096ffff
> color sel #7a81ffff
> color sel #76d6ffff
> color sel #0096ffff
> color sel #2a53e7ff
> select #3/D
1591 atoms, 1623 bonds, 196 residues, 1 model selected
> hide sel cartoons
> select #3/A
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> color sel #121ea8ff
> select #1/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> color sel #ea6e38ff
> select #2.2/D
1591 atoms, 1623 bonds, 196 residues, 1 model selected
> color sel #f3bf4cff
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 mutants/color
> proposals.cxs"
> hide #3 models
> select clear
Drag select of 5 residues
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/biological unit.cxs"
> select #1/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> color #1 #212121ff
> color #1 #424242ff
> color #1 #5e5e5eff
> select add #1
6460 atoms, 6582 bonds, 796 residues, 1 model selected
> select subtract #1
Nothing selected
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 1.cxs"
> select sequence GDPDLTLSYLSMWLHQPYVESDSRLHLESMLLETGHRAL
6340 atoms, 6500 bonds, 780 residues, 10 models selected
> color (#1#2.1-8 & sel) #941100ff
> color (#1#2.1-8 & sel) #212121ff
> color (#1#2.1-8 & sel) #941751ff
> color (#1#2.1-8 & sel) #941100ff
> color (#1#2.1-8 & sel) #ff7e79ff
> select add #1
12166 atoms, 12432 bonds, 1498 residues, 10 models selected
> select subtract #1
5706 atoms, 5850 bonds, 702 residues, 9 models selected
> select add #2
52314 atoms, 53306 bonds, 6446 residues, 10 models selected
> select subtract #2
634 atoms, 650 bonds, 78 residues, 1 model selected
> select add #3
6460 atoms, 6582 bonds, 796 residues, 1 model selected
> select subtract #3
Nothing selected
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting full
> lighting shadows false
> graphics silhouettes true
> lighting simple
[Repeated 2 time(s)]
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting soft
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 1.cxs"
> select sequence GDPDLTLSYLSMWLHQPYVESDSRLHLESMLLETGHRAL
6340 atoms, 6500 bonds, 780 residues, 10 models selected
> color (#1#2.1-8 & sel) #ecbb4aff
> color (#1#2.1-8 & sel) #f3bf4cff
> select add #3
12166 atoms, 12432 bonds, 1498 residues, 10 models selected
> select subtract #3
5706 atoms, 5850 bonds, 702 residues, 9 models selected
> select add #2
52314 atoms, 53306 bonds, 6446 residues, 10 models selected
> select subtract #2
634 atoms, 650 bonds, 78 residues, 1 model selected
> select add #1
6460 atoms, 6582 bonds, 796 residues, 1 model selected
> select subtract #1
Nothing selected
> volume hide
No volumes specified
> select ::name="ALA"
2800 atoms, 2280 bonds, 560 residues, 10 models selected
> select sequence TGDPD
680 atoms, 680 bonds, 100 residues, 10 models selected
> select ::name="ASP"
4000 atoms, 3500 bonds, 500 residues, 10 models selected
> ui tool show "Show Sequence Viewer"
[Repeated 1 time(s)]
> sequence chain #2.2/D
Alignment identifier is 2.2/D
> select add #1
10060 atoms, 9732 bonds, 1246 residues, 10 models selected
> select add #2
58540 atoms, 59588 bonds, 7214 residues, 11 models selected
> select subtract #2
6860 atoms, 6932 bonds, 846 residues, 2 models selected
> select subtract #1
400 atoms, 350 bonds, 50 residues, 1 model selected
> select add #3
6460 atoms, 6582 bonds, 796 residues, 1 model selected
> select subtract #3
Nothing selected
> select #2.2/D:18-65,74-126,144-172,176-187,196-207
1260 atoms, 1275 bonds, 154 residues, 1 model selected
> ui tool show "Selection Inspector"
> select add #2
51680 atoms, 52656 bonds, 6368 residues, 9 models selected
> select subtract #2
Nothing selected
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 2.cxs"
\u2014\u2014\u2014 End of log from Wed Sep 18 21:35:21 2024 \u2014\u2014\u2014
opened ChimeraX session
> select #1/177
Nothing selected
> select #1/Asp177
Nothing selected
> select #1:177
26 atoms, 22 bonds, 4 residues, 1 model selected
> hide #2.2 models
> show #2.2 models
> hide #!2 models
> show #!2 models
> hide #2.1 models
> show #2.1 models
> hide #2.2 models
> show #2.2 models
> hide #2.3 models
> show #2.3 models
> hide #2.3 models
> hide #2.4 models
> hide #2.5 models
> hide #2.6 models
> hide #2.7 models
> hide #2.8 models
> show #3 models
> hide #3 models
> close #2.8
> close #2.7
> close #2.6
> close #2.5
> close #2.4
> show #2.3 models
> hide #2.3 models
> close #2.3
> show #3 models
> hide #3 models
> hide #2.2 models
> show #2.2 models
> hide #2.1 models
> show #2.1 models
> close #2.1
> hide #!2 models
> hide #2.2 models
> show #2.2 models
> select #2.2:177
26 atoms, 22 bonds, 4 residues, 1 model selected
> color sel #ff7e79ff
> select #2.2:181
28 atoms, 24 bonds, 4 residues, 1 model selected
> color sel #ffd479ff
> color sel #ff7e79ff
> select #2.2:182
36 atoms, 34 bonds, 4 residues, 1 model selected
> color sel #ffd479ff
> color sel #ff7e79ff
> select #2.2:184
28 atoms, 24 bonds, 4 residues, 1 model selected
> color sel #73fdffff
> color sel #ff7e79ff
> select #2.2:185
34 atoms, 30 bonds, 4 residues, 1 model selected
> color sel #ffd479ff
> color sel #ff7e79ff
> select #2.2:188
36 atoms, 34 bonds, 4 residues, 1 model selected
> color sel #ffd479ff
> color sel #ff7e79ff
> select #2.2:191
42 atoms, 40 bonds, 4 residues, 1 model selected
> color sel #ffd479ff
> color sel #ff7e79ff
> select #2.2:193
34 atoms, 30 bonds, 4 residues, 1 model selected
> color sel #ffd479ff
> color sel #ff7e79ff
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 2.cxs"
> select #2.2:177,181,182,184,185,188,191,193
264 atoms, 246 bonds, 32 residues, 1 model selected
> color sel #fffc79ff
> color sel #f3bf4cff
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 3.cxs"
> select #2.2:175-193
646 atoms, 664 bonds, 76 residues, 1 model selected
> color sel #ff7e79ff
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 3.cxs"
> color sel #f3bf4cff
> hide #1 models
> show #1 models
> select #2.2/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> select #1/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> color sel #ffd479ff
> color sel #ff9300ff
> color sel #ea6e38ff
> select #2.2:177,181,182,184,185,188,191,193
264 atoms, 246 bonds, 32 residues, 1 model selected
> color sel #ff7e79ff
> select add #2.2
6460 atoms, 6582 bonds, 796 residues, 1 model selected
> select subtract #2.2
Nothing selected
> lighting flat
> select #2.2:177,181,182,184,185,188,191,193
264 atoms, 246 bonds, 32 residues, 1 model selected
> color sel #000000ff
> select add #2.2
6460 atoms, 6582 bonds, 796 residues, 1 model selected
> select subtract #2.2
Nothing selected
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 2.cxs"
> select #2.2:177,181,182,184,185,188,191,193
264 atoms, 246 bonds, 32 residues, 1 model selected
> color sel #f3bf4cff
> select #2.2:177,181,182,184,185,188,191,193
264 atoms, 246 bonds, 32 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> select #1:177,181,182,184,185,188,191,193
264 atoms, 246 bonds, 32 residues, 1 model selected
> sequence chain #1/C
Alignment identifier is 1/C
> select #1:63,66,68,69,72,73,76,77
258 atoms, 240 bonds, 32 residues, 1 model selected
> color sel #000000ff
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Mutant 5.cxs"
\u2014\u2014\u2014 End of log from Wed Sep 18 22:00:52 2024 \u2014\u2014\u2014
opened ChimeraX session
> select add #1
6460 atoms, 6582 bonds, 796 residues, 1 model selected
> select subtract #1
Nothing selected
> turn y 90 models #1,#2.2 center #1,#2.2
Invalid "models" argument: only initial part "#1" of atom specifier valid
> turn y 90 models #1 center #1
> turn y 90 models #2.2 center #2.2
> turn y -90 models #2.2 center #2.2
> turn y -90 models #1 center #1
> select #1:63,66,68,69,72,73,76,77
258 atoms, 240 bonds, 32 residues, 1 model selected
> color sel #eb6e37ff
> select add #1
6460 atoms, 6582 bonds, 796 residues, 1 model selected
> select subtract #1
Nothing selected
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Top.cxs"
> save /Users/lks559/Desktop/image1.png supersample 3
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Side.cxs"
> turn 90
Expected an axis vector or a keyword
> turn 90turn y 90
Expected an axis vector or a keyword
> turn y 90
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/top.cxs"
> turn y 90
[Repeated 6 time(s)]
> save /Users/lks559/Desktop/image2.png supersample 3
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/side.cxs"
> turn y 90
> save /Users/lks559/Desktop/image3.png supersample 3
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/top.cxs"
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109
> mutants/Top.cxs"
\u2014\u2014\u2014 End of log from Wed Sep 18 22:21:14 2024 \u2014\u2014\u2014
opened ChimeraX session
> graphics silhouettes width 1
> lighting model #1 depthCue true
> cartoon style width 1.5
> cartoon style nucleic width 1 thickness 0.5
> cartoon style width 1.5
> lighting multiShadow 600
> graphics silhouettes false
> lighting soft
> select #2.2
6460 atoms, 6582 bonds, 796 residues, 1 model selected
> color sel #f7f2abff
> color sel wheat
> color sel #f7f2abff
> color sel wheat
> color sel #ffffcdff
> color sel #F5DEB3
> select #1
6460 atoms, 6582 bonds, 796 residues, 1 model selected
> color sel #f7d081ff
> color sel #c6a668ff
> color sel #c5a668ff
> color sel #c2a466ff
> color sel #c3a467ff
> color sel #c8a869ff
> color sel #cbab6bff
> color sel #d1b06eff
> color sel #d2b16eff
> color sel #e0bc76ff
> color sel #f6cf81ff
> color sel #ffd786ff
> color sel #ffdd6aff
> color sel #ffde6bff
> color sel #ffdb68ff
> color sel #ffd762ff
> color sel #ffd15aff
> color sel #ffd059ff
> color sel #ffcf59ff
> color sel #ffce58ff
> color sel #ffc855ff
> color sel #ffc453ff
> color sel #ffc352ff
> color sel #ffc251ff
> color sel #ffc150ff
> color sel #ffbf4cff
> color sel #ffbd47ff
> color sel #ffba44ff
> color sel #ffb841ff
> color sel #ffb53fff
> color sel #ffb03eff
> color sel #ffac3cff
> color sel #ffa83bff
> color sel #ffa53bff
> color sel #ffa43aff
> color sel #ffa439ff
> color sel #ffa539ff
> color sel #ffa537ff
> color sel #ffa632ff
> color sel #ffa731ff
> color sel #ffa630ff
> color sel #ffa730ff
> color sel #ffa72fff
> color sel #ffa82fff
> color sel #ffa82eff
> color sel #ffaa2dff
> color sel #ffab2cff
> color sel #ffab2bff
> color sel #ffac2aff
[Repeated 1 time(s)]
> select subtract #1
Nothing selected
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/Side.cxs"
\u2014\u2014\u2014 End of log from Fri Oct 4 15:13:12 2024 \u2014\u2014\u2014
opened ChimeraX session
> select #2.2/D:177,181,182,184,185,188,191,193
71 atoms, 68 bonds, 8 residues, 1 model selected
> color sel tomato
> show sel atoms
> style sel ball
Changed 71 atom styles
> hide sel atoms
> style sel ball
Changed 71 atom styles
> show sel atoms
> style sel sphere
Changed 71 atom styles
> style sel ball
Changed 71 atom styles
> color sel byhetero
> select add #2.2
6460 atoms, 6582 bonds, 796 residues, 1 model selected
> select add #2
6460 atoms, 6582 bonds, 796 residues, 2 models selected
> select subtract #2
Nothing selected
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/Mutant2.cxs"
> save /Users/lks559/Desktop/image5.png supersample 3
> select #2.2/D:177,181,182,184,185,188,191,193
71 atoms, 68 bonds, 8 residues, 1 model selected
> hide sel atoms
> color sel #F5DEB3
> select #2.2/D:177,181,182,184,185,188,191,193
71 atoms, 68 bonds, 8 residues, 1 model selected
> select #1/C:63,66,68,69,72,73,76,77
72 atoms, 68 bonds, 8 residues, 1 model selected
> color sel tomato
> style sel ball
Changed 72 atom styles
> show sel atoms
> color sel byhetero
> select add #1
6460 atoms, 6582 bonds, 796 residues, 1 model selected
> select subtract #1
Nothing selected
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/Mutant5.cxs"
\u2014\u2014\u2014 End of log from Fri Oct 4 15:32:18 2024 \u2014\u2014\u2014
opened ChimeraX session
> transparency 80 target c
> select #2.2/D
1591 atoms, 1623 bonds, 196 residues, 1 model selected
> color sel #ecbed6ff
> select #1/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> color sel #e9ebb8ff
> select #1/C:63,66,68,69,72,73,76,77
72 atoms, 68 bonds, 8 residues, 1 model selected
> color sel tomato
> color sel byhetero
> transparency 80 target c
> graphics silhouettes true
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/Mutant5_zoom.cxs"
> select add #1
6460 atoms, 6582 bonds, 796 residues, 1 model selected
> select subtract #1
Nothing selected
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/Mutant5_zoom.cxs"
> save /Users/lks559/Desktop/image6.png supersample 3
> select #2.2/D
1591 atoms, 1623 bonds, 196 residues, 1 model selected
> color sel #ecbed6ff
> select #1/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> color sel #e9ebb8ff
> hide sel atoms
> select #2.2/D:177,181,182,184,185,188,191,193
71 atoms, 68 bonds, 8 residues, 1 model selected
> color sel tomato
> style sel ball
Changed 71 atom styles
> show sel atoms
> color sel byhetero
> transparency 80 target c
> select add #2
6460 atoms, 6582 bonds, 796 residues, 2 models selected
> select subtract #2
Nothing selected
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/Mutant2_zoom.cxs"
\u2014\u2014\u2014 End of log from Sun Oct 6 13:09:19 2024 \u2014\u2014\u2014
opened ChimeraX session
> select #2.2/D
1591 atoms, 1623 bonds, 196 residues, 1 model selected
> color sel #ecbed6ff
> select #1/C
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> color sel #e9ebb8ff
> select add #1
6460 atoms, 6582 bonds, 796 residues, 1 model selected
> select subtract #1
Nothing selected
> hide #1#2.2 atoms
> select #2.2/D:177,184,190
21 atoms, 19 bonds, 3 residues, 1 model selected
> hbonds sel reveal true
14 hydrogen bonds found
> color sel byhetero
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/interactionsite.cxs"
> select add #2
6460 atoms, 6582 bonds, 4 pseudobonds, 796 residues, 3 models selected
> select subtract #2
Nothing selected
> transparency 80 target c
> select #1/C:60-68
69 atoms, 71 bonds, 9 residues, 1 model selected
> hide sel cartoons
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/interactionsite.cxs"
[Repeated 1 time(s)]
> hide #4 models
> show #4 models
> color #4 black models
> save /Users/lks559/Desktop/image9.png supersample 3
> select #2.2/D:188
10 atoms, 10 bonds, 1 residue, 1 model selected
> ~hbonds
> undo
> select up
124 atoms, 127 bonds, 15 residues, 1 model selected
> select up
1639 atoms, 1668 bonds, 202 residues, 1 model selected
> select #2.2/D:177,184,190
21 atoms, 19 bonds, 3 residues, 1 model selected
> hbonds sel reveal true
14 hydrogen bonds found
> color #4 black models
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select add #2
6460 atoms, 6582 bonds, 4 pseudobonds, 796 residues, 3 models selected
> select subtract #2
Nothing selected
> select #2.2/D:188
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2.2/D:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2.2/D:185
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> select add #2
6460 atoms, 6582 bonds, 4 pseudobonds, 796 residues, 3 models selected
> select subtract #2
Nothing selected
> select #1/C:60-68
69 atoms, 71 bonds, 9 residues, 1 model selected
> show sel cartoons
> select add #1
6460 atoms, 6582 bonds, 796 residues, 1 model selected
> select subtract #1
Nothing selected
> save "/Users/lks559/Documents/RIBO paper/figures/CINP c1orf109 structure &
> mutants/interactionsite.cxs"
\u2014\u2014\u2014 End of log from Sun Oct 6 15:21:54 2024 \u2014\u2014\u2014
opened ChimeraX session
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2,3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
OS Loader Version: 580.140.1~8
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 2 days, 4 hours, 6 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-020
Option ROM Version: 113-D32206U1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (4)
comment:2 by , 13 months ago
| Platform: | → all |
|---|---|
| Project: | → ChimeraX |
The error only occurs when cavities are found in >1 structure. If I specify two structures but one of them has no cavities found, there is no error.
Maybe >1 structure is actually OK if it is fast. I thought >1 structure was taking forever but maybe it was because of the error and not the calculation per se.
comment:3 by , 13 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → QWebEngine crash |
comment:4 by , 13 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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