![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 6 months ago
#9106 closed defect (worksforme)
Crash opening mmCIF
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6 (2023-03-23 07:59:11 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Entered command "open 3ubx"
Fatal Python error: Segmentation fault
Thread 0x0000700009c07000 (most recent call first):
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700012e46000 (most recent call first):
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000001104ee600 (most recent call first):
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mmcif/__init__.py", line 43 in open
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 435 in remember_data_format
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 465 in collated_open
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 194 in provider_open
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/manager.py", line 198 in open_data
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mmcif/__init__.py", line 97 in fetch
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 435 in remember_data_format
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 464 in collated_open
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 154 in provider_open
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 119 in cmd_open
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 284 in event_loop
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-05-31 12:12:33.00 -0700","app_version":"1.6.0","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.6.5 (21G531)","incident_id":"8EF8AAA7-3D05-484E-8390-79086B4C6995","name":"ChimeraX"}
{
"uptime" : 3300000,
"procLaunch" : "2023-05-10 12:48:21.6081 -0700",
"procRole" : "Foreground",
"version" : 2,
"userID" : 38165,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"procStartAbsTime" : 1640786102283744,
"coalitionID" : 220053,
"osVersion" : {
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"build" : "21G531",
"releaseType" : "User"
},
"captureTime" : "2023-05-31 12:12:23.1495 -0700",
"incident" : "8EF8AAA7-3D05-484E-8390-79086B4C6995",
"bug_type" : "309",
"pid" : 10401,
"procExitAbsTime" : 3361762557890414,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.0","CFBundleVersion":"1.6.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"0E9B2CC1-C771-57CF-B5A9-6FE53DB27A51","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "1F019B8E-67A7-E877-6184-0F2FAC834424",
"wakeTime" : 1256913,
"bridgeVersion" : {"build":"20P4252","train":"7.4"},
"sleepWakeUUID" : "AE6A4B5F-F570-40D9-842E-C04C444700EB",
"sip" : "enabled",
"vmRegionInfo" : "0x50 is not in any region. Bytes before following region: 140737487478704\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7ffffff2a000-7ffffff2b000 [ 4K] r-x\/r-x SM=ALI ",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000000000000050","rawCodes":[1,80],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000050"},
"vmregioninfo" : "0x50 is not in any region. Bytes before following region: 140737487478704\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7ffffff2a000-7ffffff2b000 [ 4K] r-x\/r-x SM=ALI ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.6 (2023-03-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/kirshner1/Library/CloudStorage/OneDrive-
> LLNL/Documents/yue/quantum/a6nlu0_p1.pdb format pdb
Summary of feedback from opening
/Users/kirshner1/Library/CloudStorage/OneDrive-
LLNL/Documents/yue/quantum/a6nlu0_p1.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: 238.9 0.000 0.000
Ignored bad PDB record found on line 3
REMARK Name = LIG_min.pdb
Ignored bad PDB record found on line 5
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 6
REMARK 1 A between atoms: C1_1 and O1_5
Ignored bad PDB record found on line 7
REMARK 2 A between atoms: O1_5 and C2_6
57 messages similar to the above omitted
> hide #1 models
> show #1 models
> select add #1
65 atoms, 71 bonds, 1 residue, 1 model selected
> select subtract #1
Nothing selected
> ui mousemode right rotate
> ui mousemode right select
> ui mousemode right rotate
> close session
> open /Users/kirshner1/Library/CloudStorage/OneDrive-
> LLNL/Documents/yue/quantum/a6nlu0.cxs format session
opened ChimeraX session
> close session
> open /Users/kirshner1/Library/CloudStorage/OneDrive-
> LLNL/Documents/yue/quantum/a6nmz2_com_min.pdb format pdb
Chain information for a6nmz2_com_min.pdb #1
---
Chain | Description
? | No description available
> open /Users/kirshner1/Library/CloudStorage/OneDrive-
> LLNL/Documents/yue/quantum/A6NMZ2_p1.pdb
Summary of feedback from opening
/Users/kirshner1/Library/CloudStorage/OneDrive-
LLNL/Documents/yue/quantum/A6NMZ2_p1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK VINA RESULT: 234.4 0.000 0.000
Ignored bad PDB record found on line 2
REMARK Name = LIG_min.pdb
Ignored bad PDB record found on line 3
REMARK 7 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C4_9 and C5_10
6 messages similar to the above omitted
> surface
> ui tool show "Side View"
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> graphics silhouettes false
> surface cap false
> select add #1/?:83
15 atoms, 14 bonds, 1 residue, 1 model selected
> select clear
> save /Users/kirshner1/Library/CloudStorage/OneDrive-
> LLNL/Documents/yue/quantum/a6nmz2_com_min.cxs
> surface hidePatches
> select #1/?:9
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
164 atoms, 163 bonds, 11 residues, 2 models selected
> select up
1273 atoms, 1280 bonds, 79 residues, 2 models selected
> ~display sel
> hide sel cartoons
> select #1/?:82
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
164 atoms, 163 bonds, 11 residues, 2 models selected
> ~display sel
> hide sel cartoons
> select #1/?:150
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
190 atoms, 191 bonds, 11 residues, 2 models selected
> ~display sel
> hide sel cartoons
> select #1/?:144
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
128 atoms, 128 bonds, 8 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
48 atoms, 53 bonds, 1 residue, 1 model selected
> select down
2 atoms, 1 bond, 1 residue, 1 model selected
> select #1/?:80
13 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1/?:92
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
77 atoms, 77 bonds, 4 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #1/?:115
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
181 atoms, 180 bonds, 11 residues, 2 models selected
> select up
1273 atoms, 1280 bonds, 79 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> close session
> surface cap true
> open /Users/kirshner1/Library/CloudStorage/OneDrive-
> LLNL/Documents/yue/quantum/a6nmz2_com_min.cxs format session
> surface cap false
opened ChimeraX session
> ui mousemode right zoom
> surface hidePatches
> open /Users/kirshner1/Library/CloudStorage/OneDrive-
> LLNL/Documents/yue/quantum/sp_A6NMZ2_SNTAN_HUMA.00_xxsBL62.COMPLEX.1_2_0.1k2h_A.pdb
Chain information for sp_A6NMZ2_SNTAN_HUMA.00_xxsBL62.COMPLEX.1_2_0.1k2h_A.pdb
#3
---
Chain | Description
? | No description available
> select sidechain
3820 atoms, 3532 bonds, 316 residues, 2 models selected
> display sel
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #2 models
> show #2 models
> hide #2 models
> close session
> surface cap true
> open /Users/kirshner1/Library/CloudStorage/OneDrive-
> LLNL/Documents/yue/quantum/a6nmz2_com_min.cxs format session
> surface cap false
opened ChimeraX session
> close session
> surface cap true
> open /Users/kirshner1/Library/CloudStorage/OneDrive-
> LLNL/Documents/yue/quantum/sp_P14324_FPPS_HUMAN.17_xxsBL62.COMPLEX.2_1_0.4p0v_A.pdb
Chain information for sp_P14324_FPPS_HUMAN.17_xxsBL62.COMPLEX.2_1_0.4p0v_A.pdb
#1
---
Chain | Description
? | No description available
> ui mousemode right "rotate selected models"
> close session
> open 3ubx
===== Log before crash end =====
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
Updating list of available bundles failed: [SSL: CERTIFICATE_VERIFY_FAILED]
certificate verify failed: self signed certificate in certificate chain
(_ssl.c:1129)
UCSF ChimeraX version: 1.6 (2023-03-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
2023-05-31 12:12:42,861 WARNING Retrying (Retry(total=1, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED]
certificate verify failed: self signed certificate in certificate chain
(_ssl.c:1129)'))':
/cxservices/api/v1/chimerax/updates?uuid=157f8010-670d-5e80-b4c4-a935acbc3820&OS=macosx&OSVersion=10.16&ChimeraXVersion=1.6
2023-05-31 12:12:42,905 WARNING Retrying (Retry(total=0, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED]
certificate verify failed: self signed certificate in certificate chain
(_ssl.c:1129)'))':
/cxservices/api/v1/chimerax/updates?uuid=157f8010-670d-5e80-b4c4-a935acbc3820&OS=macosx&OSVersion=10.16&ChimeraXVersion=1.6
OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
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: 32 GB
System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0)
OS Loader Version: 540.120.3~22
Software:
System Software Overview:
System Version: macOS 12.6.5 (21G531)
Kernel Version: Darwin 21.6.0
Time since boot: 39 days 23:11
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 Family: Supported, Metal GPUFamily macOS 2
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
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: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9
ChimeraX-AddH: 2.2.3
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.3.3
ChimeraX-DockPrep: 1.1.1
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: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (3)
comment:1 by , 2 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash opening mmCIF |
comment:2 by , 2 years ago
| Status: | assigned → feedback |
|---|
Does opening 3ubx work with a fresh ChimeraX?
Note:
See TracTickets
for help on using tickets.
Reported by Dan Kirshner