![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 hours ago
Closed 24 minutes ago
#20471 closed defect (duplicate)
Crash in NSAccessibility routines
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.0-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.
I just open pdb files aand when i start to use modeller it crashes!
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{
"uptime" : 2200000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookAir10,1",
"coalitionID" : 246558,
"osVersion" : {
"train" : "macOS 14.0",
"build" : "23A344",
"releaseType" : "User"
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"captureTime" : "2026-06-08 19:05:43.2198 +0300",
"codeSigningMonitor" : 1,
"incident" : "442B1B79-0A9C-463A-98D0-4C1A522DC44D",
"pid" : 664,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-06-08 18:52:05.6196 +0300",
"procStartAbsTime" : 54914404905289,
"procExitAbsTime" : 54934024758684,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.11.1","CFBundleVersion":"1.11.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"D9C2DFFF-7582-5942-9FF5-4BFCD0FC51E8","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E7731D9C-F978-7E7E-54AA-01B65C85C99E",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"ARAA1MADX9aQBYCSARAA1MADX9awBYCSARAA1MADX9bQBYCSARAA1A==","atPC":"wANf1vAFgJIBEADUwANf1hAGgJIBEADUwANf1jAGgJIBEADUwANf1g=="},
"wakeTime" : 1135,
"sleepWakeUUID" : "42BD631E-1596-4665-9940-F4A396375786",
"sip" : "enabled",
"sroute_id" : 12,
"exception" : {"port":0,"signal":"SIGKILL","guardId":0,"codes":"0x0000000000000000, 0x0000000000000000","violations":["INVALID_OPTIONS"],"message":" INVALID_OPTIONS on mach port 0 (guarded with 0x0000000000000000)","subtype":"GUARD_TYPE_MACH_PORT","type":"EXC_GUARD","rawCodes":[0,0]},
"termination" : {"namespace":"GUARD","flags":2,"code":2305843022098595840},
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Writable regions: Total=3.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.1G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 256K 2
Activity Tracing 256K 1
CG image 656K 20
ColorSync 656K 31
CoreAnimation 992K 62
CoreGraphics 64K 4
CoreServices 832K 3
CoreUI image data 5232K 35
Foundation 32K 2
Kernel Alloc Once 32K 1
MALLOC 2.3G 90
MALLOC guard page 192K 12
Mach message 80K 4
Mach message (reserved) 16K 1 reserved VM address space (unallocated)
OpenGL GLSL 256K 3
PROTECTED_MEMORY 16K 1
STACK GUARD 56.8M 54
Stack 409.2M 54
VM_ALLOCATE 224.6M 227
VM_ALLOCATE (reserved) 128.0M 2 reserved VM address space (unallocated)
__AUTH 3235K 547
__AUTH_CONST 40.1M 808
__CTF 824 1
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__DATA_CONST 66.4M 948
__DATA_DIRTY 2888K 320
__FONT_DATA 2352 1
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__INFO_FILTER 8 1
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__OBJC_RO 70.6M 1
__OBJC_RW 2153K 1
__TEXT 1.1G 966
dyld private memory 320K 4
mapped file 233.8M 59
shared memory 3296K 27
=========== ======= =======
TOTAL 5.6G 5364
TOTAL, minus reserved VM space 5.4G 5364
",
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{
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===== Log before crash start =====
UCSF 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/berivanaksoy/Desktop/final structure.pdb" format pdb
Summary of feedback from opening /Users/berivanaksoy/Desktop/final
structure.pdb
---
warnings | End residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20 0
Start residue of secondary structure not found: HELIX 1 1 ARG A 57 LEU A 69 1
13
Start residue of secondary structure not found: HELIX 2 2 LEU A 98 ASP A 104 1
7
Start residue of secondary structure not found: HELIX 3 3 THR A 110 HIS A 131
1 22
Start residue of secondary structure not found: HELIX 4 4 LYS A 139 ASN A 141
1 3
Start residue of secondary structure not found: HELIX 5 5 VAL A 174 ARG A 179
1 6
8 messages similar to the above omitted
End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307
1 5
Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20
0
Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30
0
Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42
0
Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80
0
Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92
0
16 messages similar to the above omitted
End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307
1 5
Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20
0
Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30
0
Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42
0
Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80
0
Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92
0
16 messages similar to the above omitted
End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307
1 5
Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20
0
Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30
0
Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42
0
Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80
0
Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92
0
16 messages similar to the above omitted
End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307
1 5
Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20
0
Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30
0
Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42
0
Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80
0
Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92
0
16 messages similar to the above omitted
End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307
1 5
Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20
0
Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30
0
Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42
0
Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80
0
Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92
0
16 messages similar to the above omitted
End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307
1 5
Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20
0
Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30
0
Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42
0
Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80
0
Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92
0
16 messages similar to the above omitted
End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307
1 5
Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20
0
Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30
0
Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42
0
Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80
0
Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92
0
16 messages similar to the above omitted
End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307
1 5
Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20
0
Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30
0
Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42
0
Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80
0
Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92
0
16 messages similar to the above omitted
End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307
1 5
Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20
0
Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30
0
Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42
0
Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80
0
Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92
0
16 messages similar to the above omitted
End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307
1 5
Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20
0
Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30
0
Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42
0
Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80
0
Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92
0
25 messages similar to the above omitted
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2176 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
44 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2273 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2260 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
44 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2273 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Chain information for final structure.pdb
---
Chain | Description
1.1/A | No description available
1.2/A 1.9/A | No description available
1.3/A | No description available
1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A | No description available
1.15/A | No description available
Computing secondary structure
> hide #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #1.4 models
> hide #1.5 models
> hide #1.6 models
> hide #1.7 models
> hide #!1.9 models
> hide #1.8 models
> hide #1.10 models
> hide #1.11 models
> hide #1.12 models
> hide #1.13 models
> hide #1.14 models
> hide #1.15 models
> log metadata
No models had metadata
> show #1.15 models
> log metadata
No models had metadata
> info attributes models #1.*
Expected a models specifier or a keyword
> hide #1.15 models
> show #1.14 models
> hide #1.14 models
> show #1.13 models
> hide #1.13 models
> show #1.12 models
> hide #1.12 models
> show #1.11 models
> hide #1.11 models
> show #1.10 models
> hide #1.10 models
> show #!1.9 models
> hide #!1.9 models
> view #1.3 clip false
> close
> open CT7030
'CT7030' has no suffix
> open 8p4z
8p4z title:
Crystal structure of the human CDK7 kinase domain in complex with LDC4297
[more info...]
Chain information for 8p4z #1
---
Chain | Description | UniProt
A B | Cyclin-dependent kinase 7 | CDK7_HUMAN 10-311
Non-standard residues in 8p4z #1
---
1PE — pentaethylene glycol (PEG400)
GOL — glycerol (glycerin; propane-1,2,3-triol)
PGE — triethylene glycol
WZ8 —
2-[(3R)-piperidin-3-yl]oxy-8-propan-2-yl-N-[(2-pyrazol-1-ylphenyl)methyl]pyrazolo[1,5-a][1,3,5]triazin-4-amine
8p4z mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
22 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
4531 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> open 8r99
8r99 title:
A soakable crystal form of human CDK7 in complex with AMP-PNP [more info...]
Chain information for 8r99 #2
---
Chain | Description | UniProt
A | Cyclin-dependent kinase 7 | CDK7_HUMAN 1-346
Non-standard residues in 8r99 #2
---
ANP — phosphoaminophosphonic acid-adenylate ester
MG — magnesium ion
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2260 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> open 8r9a
Summary of feedback from opening 8r9a fetched from pdb
---
warning | Atom H32 is not in the residue template for I74 /A:402
8r9a title:
A soakable crystal form of human CDK7 in complex with AMP-PNP [more info...]
Chain information for 8r9a #3
---
Chain | Description | UniProt
A | Cyclin-dependent kinase 7 | CDK7_HUMAN 1-346
Non-standard residues in 8r9a #3
---
I74 — (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-
pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol
PEG — di(hydroxyethyl)ether
44 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2273 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> hide atoms
> delete #3/B
> delete ~/A
> delete solvent
> matchmaker #1 to #3
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 8r9a, chain A (#3) with 8p4z, chain A (#1), sequence alignment
score = 1463.7
RMSD between 249 pruned atom pairs is 0.532 angstroms; (across all 269 pairs:
1.793)
> open
> ./Gene433_FinalReport_Documents_Berivan_Aksoy/Sequences/cdk20_isoform3_Homosapiens.fasta
Summary of feedback from opening
./Gene433_FinalReport_Documents_Berivan_Aksoy/Sequences/cdk20_isoform3_Homosapiens.fasta
---
note | Alignment identifier is cdk20_isoform3_Homosapiens.fasta
Opened 1 sequence from cdk20_isoform3_Homosapiens.fasta
> sequence associate #1/A,2/A,3/A cdk20_isoform3_Homosapiens.fasta:1
Associated 8p4z chain A to NP_001034892.1 cyclin-dependent kinase 20 isoform 3
[Homo sapiens] with 173 mismatches and/or gaps
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.9
Locale: 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 Air
Model Identifier: MacBookAir10,1
Model Number: MGN63TU/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.1.1
OS Loader Version: 10151.1.1
Software:
System Software Overview:
System Version: macOS 14.0 (23A344)
Kernel Version: Darwin 23.0.0
Time since boot: 163 days, 1 hour, 17 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
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 , 35 minutes ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in NSAccessibility routines |
comment:2 by , 24 minutes ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Probable Qt bug.