Opened 3 years ago

Closed 3 years ago

#8149 closed defect (can't reproduce)

Crash in event loop after volume step 1 on .mtz data

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc: Tristan Croll
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: 1.4rc202205140117 (2022-05-14 01:17:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x0000000202d3b2c0 (most recent call first):
  File "/Applications/ChimeraX-1.4-rc2022.05.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
  File "/Applications/ChimeraX-1.4-rc2022.05.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
  File "/Applications/ChimeraX-1.4-rc2022.05.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in 
  File "/Applications/ChimeraX-1.4-rc2022.05.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.4-rc2022.05.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


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{
  "uptime" : 100000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,3",
  "coalitionID" : 2688,
  "osVersion" : {
    "train" : "macOS 13.0.1",
    "build" : "22A400",
    "releaseType" : "User"
  },
  "captureTime" : "2022-12-08 12:51:13.6883 +0200",
  "incident" : "BB6A97A8-F8DC-4CA7-BDFF-036EBC68A5C1",
  "pid" : 52180,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2022-12-08 12:46:35.6083 +0200",
  "procStartAbsTime" : 2393481953782,
  "procExitAbsTime" : 2400155805085,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.4-rc2022.05.14.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"EE7F4037-FBBD-5660-9106-8AF79EE4F2A1","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "7C7118B4-D68D-E341-76AD-DC7A3EEE0086",
  "wakeTime" : 3082,
  "sleepWakeUUID" : "C6F3AB93-32AF-43EE-921E-EAF18F445D4A",
  "sip" : "enabled",
  "vmRegionInfo" : "0x40 is not in any region.  Bytes before following region: 140723072876480\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffca4c54000-7ffcabb0c000 [110.7M] r-x\/r-x SM=COW  ...t_id=54a4df31",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000040","rawCodes":[1,64],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000040"},
  "vmregioninfo" : "0x40 is not in any region.  Bytes before following region: 140723072876480\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffca4c54000-7ffcabb0c000 [110.7M] r-x\/r-x SM=COW  ...t_id=54a4df31",
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  "faultingThread" : 0,
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    "source" : "P",
    "arch" : "x86_64",
    "base" : 5198385152,
    "size" : 165068800,
    "uuid" : "c9795830-14cd-3b40-983d-a3143cd9cbd9",
    "path" : "\/Applications\/ChimeraX-1.4-rc2022.05.14.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703637368832,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 16797687,
    "uuid" : "817d572e-eb8c-3999-b7a0-68e1c4b47266",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2299"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4911489024,
    "size" : 5226496,
    "uuid" : "97d356c9-7652-3ff7-be10-198e30670243",
    "path" : "\/Applications\/ChimeraX-1.4-rc2022.05.14.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
    "name" : "QtCore"
  }
],
  "sharedCache" : {
  "base" : 140703582044160,
  "size" : 21474836480,
  "uuid" : "7b321622-762b-3cdc-9d76-14f1310c0a31"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=3.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.4G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               768K        6 \nActivity Tracing                   256K        1 \nCG backing stores                 3520K        4 \nCG image                          6404K       44 \nColorSync                          252K       29 \nCoreAnimation                     3492K       30 \nCoreGraphics                        12K        2 \nCoreUI image data                 4896K       37 \nFoundation                          32K        2 \nKernel Alloc Once                    8K        1 \nMALLOC                             1.7G      224 \nMALLOC guard page                  192K        9 \nMALLOC_MEDIUM (reserved)         624.0M        8         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           256.0M        1         reserved VM address space (unallocated)\nMach message                        24K        6 \nOpenGL GLSL                        384K        4 \nRosetta Arena                     4096K        2 \nRosetta Generic                   1680K      417 \nRosetta IndirectBranch            2048K        1 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack               940K       94 \nRosetta Thread Context             940K       94 \nSTACK GUARD                         40K       10 \nStack                            166.7M       48 \nStack Guard                       56.2M       38 \nVM_ALLOCATE                      136.7M      287 \nVM_ALLOCATE (reserved)           384.1M       19         reserved VM address space (unallocated)\n__CTF                               756        1 \n__DATA                            48.4M      790 \n__DATA_CONST                      39.9M      391 \n__DATA_DIRTY                      1835K      226 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       207.4M      186 \n__OBJC_RO                         65.1M        1 \n__OBJC_RW                         1980K        2 \n__TEXT                             1.0G      791 \ndyld private memory                512K        3 \nmapped file                        4.6G     1814 \nshared memory                     3164K       32 \nunshared pmap                     14.6M       10 \n===========                     =======  ======= \nTOTAL                              9.4G     5668 \nTOTAL, minus reserved VM space     8.1G     5668 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "61675b89201f677a9a4cbd65",
      "factorPackIds" : {
        "HEALTH_FEATURE_AVAILABILITY" : "63605e98c8a2104545a56f10"
      },
      "deploymentId" : 240000045
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      "rolloutId" : "60f8ddccefea4203d95cbeef",
      "factorPackIds" : {

      },
      "deploymentId" : 240000021
    }
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  "experiments" : [

  ]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.4rc202205140117 (2022-05-14)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/nitsanyehishalom/Desktop/Studys/MS.c./Reserach/Results semester
> 3/Structures/WT 5-13.pdb" format pdb

WT 5-13.pdb title:  
\--- [more info...]  
  
Chain information for WT 5-13.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Non-standard residues in WT 5-13.pdb #1  
---  
CRO — (CRO)  
NA — (NA)  
SO4 — (SO4)  
  

> open "/Users/nitsanyehishalom/Desktop/Studys/MS.c./Reserach/Results semester
> 3/Structures/WT 5-13.mtz"

Summary of feedback from opening
/Users/nitsanyehishalom/Desktop/Studys/MS.c./Reserach/Results semester
3/Structures/WT 5-13.mtz  
---  
warnings | WARNING: multiple experimental reflection datasets found:  
(dataset) HKL_base,  
(dataset) F, SIGF  
Automatically choosing "(dataset) F, SIGF".  
No free flags detected in this dataset! Automatically generated a new random
set with 2119 free from 119546 observed reflections. You should save your data
to a new MTZ file and use this for any future rebuilding/refinement.  
note | Discarding unrecognised/unsupported data array /DEFAULT/1/FOM W  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 78,74,78, pixel
0.324,0.326,0.315, shown at level 0.934, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 78,74,78, pixel
0.324,0.326,0.315, shown at level -0.206,0.206, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_25 as #1.1.1.4, grid size 78,74,78, pixel
0.324,0.326,0.315, shown at level 0.211, step 1, values float32  
Opened (STATIC) (dataset) FC, PHIC as #1.1.1.5, grid size 78,74,78, pixel
0.324,0.326,0.315, shown at level 1.02, step 1, values float32  
Opened (STATIC) (dataset) FC_ALL, PHIC_ALL as #1.1.1.6, grid size 78,74,78,
pixel 0.324,0.326,0.315, shown at level -1.1,1.1, step 1, values float32  
Opened (STATIC) (dataset) FWT, PHWT as #1.1.1.7, grid size 78,74,78, pixel
0.324,0.326,0.315, shown at level 0.935, step 1, values float32  
Opened (STATIC) (dataset) DELFWT, PHDELWT as #1.1.1.8, grid size 78,74,78,
pixel 0.324,0.326,0.315, shown at level -0.339,0.339, step 1, values float32  
Opened (STATIC) (dataset) FAN, PHAN as #1.1.1.9, grid size 78,74,78, pixel
0.324,0.326,0.315, shown at level -0.0611,0.0611, step 1, values float32  
Opened (STATIC) (dataset) DELFAN, PHDELAN as #1.1.1.10, grid size 78,74,78,
pixel 0.324,0.326,0.315, shown at level -0.0611,0.0611, step 1, values float32  
Opened (STATIC) (dataset) FC_ALL_LS, PHIC_ALL_LS as #1.1.1.11, grid size
78,74,78, pixel 0.324,0.326,0.315, shown at level -1.11,1.11, step 1, values
float32  
WT 5-13.pdb title:  
\--- [more info...]  
  
Chain information for WT 5-13.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
  
Non-standard residues in WT 5-13.pdb #1.2  
---  
CRO — (CRO)  
NA — (NA)  
SO4 — (SO4)  
  
Opened crystallographic dataset from
/Users/nitsanyehishalom/Desktop/Studys/MS.c./Reserach/Results semester
3/Structures/WT 5-13.mtz  
Found experimental reflection data:  
(dataset) F, SIGF  
Rwork: 0.1873; Rfree: 0.1853  
Generated maps:  
Reflection Data  
(LIVE) 2mFo-DFc  
(LIVE) mFo-DFc  
(LIVE) 2mFo-DFc_smooth_25  
(STATIC) (dataset) FC, PHIC  
(STATIC) (dataset) FC_ALL, PHIC_ALL  
(STATIC) (dataset) FWT, PHWT  
(STATIC) (dataset) DELFWT, PHDELWT  
(STATIC) (dataset) FAN, PHAN  
(STATIC) (dataset) DELFAN, PHDELAN  
(STATIC) (dataset) FC_ALL_LS, PHIC_ALL_LS  
Any unwanted maps may be safely closed via the Model panel.  

> ui tool show "Surface Zone"

> ui tool show "Map Coordinates"

Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 10 maps.  

> select #1.2 /A :210

7 atoms, 7 bonds, 1 residue, 1 model selected  

Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 10 maps.  

> transparency 0

> view sel

> transparency 50

> transparency 0

> transparency 50

> hide ribbons

> select down

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

77 atoms, 78 bonds, 11 residues, 1 model selected  

> hide ~sel ribbons

> hide ~sel

> ui tool show "Volume Viewer"

> volume #1.1.1.2 level 0.2708

> volume #1.1.1.2 level 0.2822

> volume #1.1.1.2 style mesh

> close #1.1.1.3

Deleting (LIVE) mFo-DFc  

> close #1.1.1.4

Deleting (LIVE) 2mFo-DFc_smooth_25  

> close #1.1.1.5

> close #1.1.1.6

> close #1.1.1.7

> close #1.1.1.8

> close #1.1.1.9

> close #1.1.1.10

> close #1.1.1.11

> surface dust #1.1.1.2 size 3.26

> volume #1.1.1.2 level 0.2156

> volume step 2

> volume step 1


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

Log:
UCSF ChimeraX version: 1.4rc202205140117 (2022-05-14)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

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: MacBookPro18,3
      Model Number: Z15G000MKAE/A
      Chip: Unknown
      Total Number of Cores: 8 (6 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0.1 (22A400)
      Kernel Version: Darwin 22.1.0
      Time since boot: 7 days, 18 hours, 27 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          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-Clipper: 0.18.0
    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: 1.4rc202205140117
    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
    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: 1.18.2
    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: 3.6.0
    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: 22.3.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    Send2Trash: 1.8.0
    SEQCROW: 1.5.10
    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: 5.2.0
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash in event loop after volume step 1

comment:2 by Tom Goddard, 3 years ago

Cc: Tristan Croll added
Resolution: → can't reproduce
Status: assigned → closed
Summary: Crash in event loop after volume step 1 → Crash in event loop after volume step 1 on .mtz data

C++ stack trace has no useful info.

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