Opened 3 years ago

Closed 3 years ago

#7128 closed defect (can't reproduce)

Crash saving STL

Reported by: j.kenkel@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc: Greg Couch
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: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error

Thread 0x000070002672b000 (most recent call first):
  File "/private/var/folders/dy/d0kyy8kx0rb2t6bxj3bmf7tw0000gn/T/AppTranslocation/71995A8B-009A-4441-A6A7-53DF6CD2D1F5/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
  File "/private/var/folders/dy/d0kyy8kx0rb2t6bxj3bmf7tw0000gn/T/AppTranslocation/71995A8B-009A-4441-A6A7-53DF6CD2D1F5/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/private/var/folders/dy/d0kyy8kx0rb2t6bxj3bmf7tw0000gn/T/AppTranslocation/71995A8B-009A-4441-A6A7-53DF6CD2D1F5/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/private/var/folders/dy/d0kyy8kx0rb2t6bxj3bmf7tw0000gn/T/AppTranslocation/71995A8B-009A-4441-A6A7-53DF6CD2D1F5/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700025728000 (most recent call first):
  File "/private/var/folders/dy/d0kyy8kx0rb2t6bxj3bmf7tw0000gn/T/AppTranslocation/71995A8B-009A-4441-A6A7-53DF6CD2D1F5/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
  File "/private/var/folders/dy/d0kyy8kx0rb2t6bxj3bmf7tw0000gn/T/AppTranslocation/71995A8B-009A-4441-A6A7-53DF6CD2D1F5/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/private/var/folders/dy/d0kyy8kx0rb2t6bxj3bmf7tw0000gn/T/AppTranslocation/71995A8B-009A-4441-A6A7-53DF6CD2D1F5/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/private/var/folders/dy/d0kyy8kx0rb2t6bxj3bmf7tw0000gn/T/AppTranslocation/71995A8B-009A-4441-A6A7-53DF6CD2D1F5/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700024725000 (most recent call first):
  File "/private/var/folders/dy/d0kyy8kx0rb2t6bxj3bmf7tw0000gn/T/AppTranslocation/71995A8B-009A-4441-A6A7-53DF6CD2D1F5/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
  File "/private/var/folders/dy/d0kyy8kx0rb2t6bxj3bmf7tw0000gn/T/AppTranslocation/71995A8B-009A-4441-A6A7-53DF6CD2D1F5/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
  File "/private/var/folders/dy/d0kyy8kx0rb2t6bxj3bmf7tw0000gn/T/AppTranslocation/71995A8B-009A-4441-A6A7-53DF6CD2D1F5/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
  File "/private/var/folders/dy/d0kyy8kx0rb2t6bxj3bmf7tw0000gn/T/AppTranslocation/71995A8B-009A-4441-A6A7-53DF6CD2D1F5/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
  File "/private/var/folders/dy/d0kyy8kx0rb2t6bxj3bmf7tw0000gn/T/AppTranslocation/71995A8B-009A-4441-A6A7-53DF6CD2D1F5/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/private/var/folders/dy/d0kyy8kx0rb2t6bxj3bmf7tw0000gn/T/AppTranslocation/71995A8B-009A-4441-A6A7-53DF6CD2D1F5/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/private/var/folders/dy/d0kyy8kx0rb2t6bxj3bmf7tw0000gn/T/AppTranslocation/71995A8B-009A-4441-A6A7-53DF6CD2D1F5/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py

{"app_name":"ChimeraX","timestamp":"2022-06-19 16:56:52.00 -0400","app_version":"","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"","platform":1,"share_with_app_devs":0,"is_first_party":1,"bug_type":"309","os_version":"macOS 12.4 (21F79)","incident_id":"2CEFCAB6-F466-4DE7-ABAB-A99BFB5F45F2","name":"ChimeraX"}
{
  "uptime" : 250000,
  "procLaunch" : "2022-06-19 11:38:46.4117 -0400",
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro16,1",
  "procStartAbsTime" : 238551105287858,
  "coalitionID" : 68250,
  "osVersion" : {
    "train" : "macOS 12.4",
    "build" : "21F79",
    "releaseType" : "User"
  },
  "captureTime" : "2022-06-19 16:56:51.8249 -0400",
  "incident" : "2CEFCAB6-F466-4DE7-ABAB-A99BFB5F45F2",
  "bug_type" : "309",
  "pid" : 97789,
  "procExitAbsTime" : 252069167717359,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/private\/var\/folders\/*\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "F38B6B46-16FC-0391-563E-F03D6A5ED3B0",
  "wakeTime" : 4500,
  "bridgeVersion" : {"build":"19P5071","train":"6.5"},
  "sleepWakeUUID" : "1D4809F0-410E-495B-AA95-5F4BAFF8BF95",
  "sip" : "enabled",
  "vmRegionInfo" : "0x10cf2a2e9 is in 0x10cdb0000-0x10d019000;  bytes after start: 1549033  bytes before end: 978198\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      ColorSync                   10cdae000-10cdb0000    [    8K] r--\/r-- SM=COW  \n--->  mapped file                 10cdb0000-10d019000    [ 2468K] r-x\/rwx SM=COW  ...t_id=bae9bee1\n      mapped file                 10d019000-10d053000    [  232K] rw-\/rwx SM=COW  ...t_id=b6c35fe1",
  "isCorpse" : 1,
  "exception" : {"codes":"0x000000000000000a, 0x000000010cf2a2e9","rawCodes":[10,4512195305],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_MEMORY_ERROR at 0x000000010cf2a2e9"},
  "termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"exc handler","byPid":97789},
  "vmregioninfo" : "0x10cf2a2e9 is in 0x10cdb0000-0x10d019000;  bytes after start: 1549033  bytes before end: 978198\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      ColorSync                   10cdae000-10cdb0000    [    8K] r--\/r-- SM=COW  \n--->  mapped file                 10cdb0000-10d019000    [ 2468K] r-x\/rwx SM=COW  ...t_id=bae9bee1\n      mapped file                 10d019000-10d053000    [  232K] rw-\/rwx SM=COW  ...t_id=b6c35fe1",
  "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" : [{"triggered":true,"id":2880555,"name":"CrBrowserMain","threadState":{"r13":{"value":4512592363},"rax":{"value":214},"rflags":{"value":66054},"cpu":{"value":1},"r14":{"value":140223033830960},"rsi":{"value":140223033830960},"r8":{"value":140222763663176},"cr2":{"value":4512195305},"rdx":{"value":0},"r10":{"value":4654315180,"symbolLocation":172,"symbol":"_main_thread"},"r9":{"value":8022828266574728919},"r15":{"value":9},"rbx":{"value":140704698624224},"trap":{"value":14,"description":"(no mapping for user instruction 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===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/jeffreykenkel/Downloads/7x2f.pdb

7x2f.pdb title:  
Cryo-em structure of the dopamine and LY3154207-bound D1 dopamine receptor and
mini-GS complex [more info...]  
  
Chain information for 7x2f.pdb #1  
---  
Chain | Description | UniProt  
A | guanine nucleotide-binding protein G(S) subunit α isoforms short, isoform
gnas-2 of guanine nucleotide-binding protein G(S) subunit α isoforms short |  
B | transducin β chain 1 | GBB1_HUMAN  
D | G γ-I | GBG2_HUMAN  
E | NANOBODY35 |  
F | dopamine D1 receptor | DRD1_HUMAN  
  
Non-standard residues in 7x2f.pdb #1  
---  
CLR — cholesterol  
G4C —
2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-3-oxidanyl-
butyl)-3,4-dihydro-1H-isoquinolin-2-yl]ethanone  
LDP — L-dopamine (dopamine)  
  

> select /D

434 atoms, 440 bonds, 57 residues, 1 model selected  

> select /A

1896 atoms, 1933 bonds, 1 pseudobond, 228 residues, 2 models selected  

> select /F

2339 atoms, 2405 bonds, 3 pseudobonds, 286 residues, 2 models selected  

> select ~sel

5900 atoms, 6012 bonds, 1 pseudobond, 754 residues, 2 models selected  

> surface hidePatches (#!1 & sel)

> cartoon hide (#!1 & sel)

> undo

> select ~sel

5900 atoms, 6012 bonds, 1 pseudobond, 754 residues, 2 models selected  

> hide (#!1 & sel) target a

> toolshed show

Window position QRect(1887,527 100x30) outside any known screen, using primary
screen  

> rainbow sel

> color sel bynucleotide

> close

> show # target m

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> undo

Undo failed, probably because structures have been modified.  

> undo

Undo failed, probably because structures have been modified.  

> show # target m

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> open /Users/jeffreykenkel/Downloads/7x2f.pdb format pdb

7x2f.pdb title:  
Cryo-em structure of the dopamine and LY3154207-bound D1 dopamine receptor and
mini-GS complex [more info...]  
  
Chain information for 7x2f.pdb #1  
---  
Chain | Description | UniProt  
A | guanine nucleotide-binding protein G(S) subunit α isoforms short, isoform
gnas-2 of guanine nucleotide-binding protein G(S) subunit α isoforms short |  
B | transducin β chain 1 | GBB1_HUMAN  
D | G γ-I | GBG2_HUMAN  
E | NANOBODY35 |  
F | dopamine D1 receptor | DRD1_HUMAN  
  
Non-standard residues in 7x2f.pdb #1  
---  
CLR — cholesterol  
G4C —
2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-3-oxidanyl-
butyl)-3,4-dihydro-1H-isoquinolin-2-yl]ethanone  
LDP — L-dopamine (dopamine)  
  

> select /F

2339 atoms, 2405 bonds, 3 pseudobonds, 286 residues, 2 models selected  

> select ~sel

5900 atoms, 6012 bonds, 1 pseudobond, 754 residues, 2 models selected  

> hide (#!1 & sel) target a

> save "/Users/jeffreykenkel/Downloads/Dopamine D1 receptor CryoEM.stl"

> undo

> select /D

434 atoms, 440 bonds, 57 residues, 1 model selected  

> select /A

1896 atoms, 1933 bonds, 1 pseudobond, 228 residues, 2 models selected  

> select ~sel

6343 atoms, 6484 bonds, 3 pseudobonds, 812 residues, 2 models selected  

> hide (#!1 & sel) target a

> undo

> redo

> show target m

> view clip false

> save "/Users/jeffreykenkel/Downloads/Guanine Nucleotide Binding
> Structure.stl"


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/jeffreykenkel/Downloads/7x2f.pdb

7x2f.pdb title:  
Cryo-em structure of the dopamine and LY3154207-bound D1 dopamine receptor and
mini-GS complex [more info...]  
  
Chain information for 7x2f.pdb #1  
---  
Chain | Description | UniProt  
A | guanine nucleotide-binding protein G(S) subunit α isoforms short, isoform
gnas-2 of guanine nucleotide-binding protein G(S) subunit α isoforms short |  
B | transducin β chain 1 | GBB1_HUMAN  
D | G γ-I | GBG2_HUMAN  
E | NANOBODY35 |  
F | dopamine D1 receptor | DRD1_HUMAN  
  
Non-standard residues in 7x2f.pdb #1  
---  
CLR — cholesterol  
G4C —
2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-3-oxidanyl-
butyl)-3,4-dihydro-1H-isoquinolin-2-yl]ethanone  
LDP — L-dopamine (dopamine)  
  




OpenGL version: 4.1 ATI-4.8.54
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
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: 64 GB
      System Firmware Version: 1731.120.10.0.0 (iBridge: 19.16.15071.0.0,0)
      OS Loader Version: 540.120.3~6

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F79)
      Kernel Version: Darwin 21.5.0
      Time since boot: 7 days 7:36

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: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
File attachment: 7x2f.pdb

7x2f.pdb​

Attachments (1)

7x2f.pdb​ (963.3 KB ) - added by j.kenkel@… 3 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (3)

by j.kenkel@…, 3 years ago

Attachment: 7x2f.pdb​ added

Added by email2trac

comment:1 by Eric Pettersen, 3 years ago

Cc: Greg Couch added
Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash saving STL

Reported by Jeff Kenkel

comment:2 by Tom Goddard, 3 years ago

Resolution: → can't reproduce
Status: assigned → closed

The last command before the crash was saving an STL file. But the Mac crash traceback shows it was in some multithreading code, possibly associated with the Toolshed html window. The traceback is missing most of the function names but includes

ThreadPoolServiceThread
Chrome_IOThread
NetworkConfigWatcher

The Qt window toolkit uses Chrome for html widgets like the Toolshed panel. Unfortunately it seems to be involved in various crashes that we cannot track down and are bugs in the Qt window toolkit.

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