Opened 15 months ago

Closed 15 months ago

Last modified 15 months ago

#15660 closed defect (can't reproduce)

Crash in garbage collection

Reported by: carlton.petermark.3v@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-12.7.1-x86_64-i386-64bit
ChimeraX Version: 1.9.dev202405110020 (2024-05-11 00:20:53 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.

I clicked "Color PAE domains" from the PAE viewer while I already had a selection established in the viewer.
Fatal Python error: Segmentation fault

Current thread 0x000000011c03f600 (most recent call first):
  Garbage-collecting
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/networkx/utils/mapped_queue.py", line 159 in 
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/networkx/utils/mapped_queue.py", line 159 in __init__
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/networkx/algorithms/community/modularity_max.py", line 105 in 
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/networkx/algorithms/community/modularity_max.py", line 105 in _greedy_modularity_communities_generator
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/networkx/algorithms/community/modularity_max.py", line 333 in greedy_modularity_communities
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/networkx/utils/backends.py", line 633 in __call__
  File " compilation 4", line 3 in argmap_greedy_modularity_communities_1
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/pae.py", line 1166 in pae_domains
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/pae.py", line 956 in color_domains
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/pae.py", line 595 in _color_domains
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 285 in event_loop
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1006 in init
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1169 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.atom_search.ast, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 56)


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{
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  "procLaunch" : "2024-07-24 16:49:33.4494 +0900",
  "procRole" : "Foreground",
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  "captureTime" : "2024-07-24 17:04:47.5711 +0900",
  "incident" : "B33EDAE2-F220-42A6-B8AF-8699FC5E4509",
  "bug_type" : "309",
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  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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  "parentPid" : 1,
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  "crashReporterKey" : "B9141A2B-BB6A-AD8E-3FB5-46A0DD310398",
  "sip" : "disabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 140737487150935\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      VM_ALLOCATE              7fffffeda000-7fffffedb000 [    4K] r-x\/r-x SM=ALI  ",
  "isCorpse" : 1,
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  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 140737487150935\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      VM_ALLOCATE              7fffffeda000-7fffffedb000 [    4K] r-x\/r-x SM=ALI  ",
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  "faultingThread" : 0,
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    "size" : 5373952,
    "uuid" : "f4950342-54e3-3755-a88f-e2a6406c1fc3",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
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    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets",
    "name" : "QtWidgets"
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    "size" : 2867200,
    "uuid" : "04d3e498-8e36-3f03-9aa5-8a19040cc57f",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
    "name" : "QtWidgets.abi3.so"
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    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
    "name" : "QtGui"
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    "size" : 655360,
    "uuid" : "a9df58b1-89b1-36c8-9d9e-fe251bf025f2",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
    "name" : "libqcocoa.dylib"
  },
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    "arch" : "x86_64h",
    "base" : 140703624601600,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 5255168,
    "uuid" : "fb79a14a-fda9-3a3b-bc97-6eb525b794a6",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "1866"
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    "arch" : "x86_64",
    "base" : 140703772438528,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 3096576,
    "uuid" : "913d3d2e-4e4c-3907-98fe-8f4abd551297",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
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    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 15269888,
    "uuid" : "461a4d7c-b3e3-3cbc-92b7-a2a419007281",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2113.60.148"
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    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 16384,
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    "name" : "ChimeraX",
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    "uuid" : "771e1916-3a62-34cd-8488-c1021053c7fa",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
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    "size" : 66404352,
    "uuid" : "7048d1fd-b9a9-3f6a-b752-ae8be69f6c3f",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
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    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
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    "arch" : "x86_64",
    "base" : 140703623602176,
    "size" : 364544,
    "uuid" : "a372724f-4642-369b-a01b-28e1f5e83ff1",
    "path" : "\/usr\/lib\/libc++.1.dylib",
    "name" : "libc++.1.dylib"
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],
  "sharedCache" : {
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  "size" : 19331678208,
  "uuid" : "172bd7f4-7e24-3286-a975-45e4e44c23c1"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=1.8G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.8G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               512K        4 \nActivity Tracing                   256K        1 \nCG backing stores                 6720K        8 \nCG image                           344K       30 \nColorSync                          232K       28 \nCoreAnimation                      332K       20 \nCoreGraphics                        16K        3 \nCoreServices                       668K        3 \nCoreUI image data                 4396K       33 \nFoundation                          68K        2 \nIOKit                             15.5M        2 \nKernel Alloc Once                    8K        1 \nMALLOC                           978.4M      167 \nMALLOC guard page                   48K       10 \nMALLOC_MEDIUM (reserved)         256.0M        4         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           128.0M        1         reserved VM address space (unallocated)\nMach message                        16K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        136K       34 \nStack                            175.3M       35 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      230.1M      214 \nVM_ALLOCATE (reserved)            32.0M        1         reserved VM address space (unallocated)\n__CTF                               756        1 \n__DATA                            51.7M      704 \n__DATA_CONST                      40.7M      401 \n__DATA_DIRTY                      1778K      229 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       676.7M      159 \n__OBJC_RO                         82.9M        1 \n__OBJC_RW                         3200K        2 \n__TEXT                           848.9M      704 \n__UNICODE                          592K        1 \ndyld private memory               1056K        2 \nmapped file                      186.1M       48 \nshared memory                     3484K       24 \n===========                     =======  ======= \nTOTAL                              3.7G     2886 \nTOTAL, minus reserved VM space     3.3G     2886 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "60f8ddccefea4203d95cbeef",
      "factorPackIds" : {

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      "factorPackIds" : {

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      "deploymentId" : 240000614
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  "experiments" : [
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      "experimentId" : "6639bc6ba73d460582162323",
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}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.9.dev202405110020 (2024-05-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/pcarlton/Downloads/fold_spo_11_dsb_1/fold_spo_11_dsb_1_model_0.cif

Chain information for fold_spo_11_dsb_1_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  

> color bychain

> alphafold pae #1 file
> /Users/pcarlton/Downloads/fold_spo_11_dsb_1/fold_spo_11_dsb_1_full_data_0.json

> alphafold pae #1 colorDomains true

> interfaces ~solvent

1 buried areas: A B 3150  

> color modify sel lightness +10

> color modify sel lightness +80

> color modify sel lightness +50

> color modify sel lightness +60

> color modify sel lightness +70

> color modify sel saturation +50

> select clear

> ui tool show Contacts

> contacts sel restrict cross resSeparation 8 interModel false intraMol false
> ignoreHiddenModels true select true dashes 1 reveal true

No atoms match given atom specifier  

> contacts resSeparation 8 interModel false intraMol false ignoreHiddenModels
> true select true dashes 1 reveal true

229 contacts  

> close

> open
> /Users/pcarlton/Downloads/fold_spo_11_biggestdeltac_dsb_1/fold_spo_11_biggestdeltac_dsb_1_model_0.cif

Chain information for fold_spo_11_biggestdeltac_dsb_1_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  

> alphafold pae #1 file
> /Users/pcarlton/Downloads/fold_spo_11_biggestdeltac_dsb_1/fold_spo_11_biggestdeltac_dsb_1_full_data_0.json

> alphafold pae #1 colorDomains true

> color bychain

> contacts resSeparation 8 interModel false intraMol false ignoreHiddenModels
> true select true dashes 1 reveal true

240 contacts  

> color modify sel saturation +50

> color modify sel saturation +150

> color modify sel saturation +10

> name frozen c sel

> select clear

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for fold_spo_11_biggestdeltac_dsb_1_model_0.cif_A SES surface
#1.2: minimum, -17.76, mean -1.69, maximum 11.48  
Coulombic values for fold_spo_11_biggestdeltac_dsb_1_model_0.cif_B SES surface
#1.3: minimum, -14.77, mean 0.05, maximum 17.95  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select clear

> contacts resSeparation 8 interModel false intraMol false ignoreHiddenModels
> true select true dashes 1 reveal true

240 contacts  

> color modify sel saturation +10

> color modify sel saturation 0

> select clear

> transparency 50

> close

> open
> /Users/pcarlton/Downloads/fold_spo_11_dsb_1ph/fold_spo_11_dsb_1ph_model_0.cif

Chain information for fold_spo_11_dsb_1ph_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  

> alphafold pae #1 file
> /Users/pcarlton/Downloads/fold_spo_11_dsb_1ph/fold_spo_11_dsb_1ph_full_data_0.json

> color #1/A:404-423 lime


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

Log:
UCSF ChimeraX version: 1.9.dev202405110020 (2024-05-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon R9 M380 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac17,1
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 3.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 32 GB
      System Firmware Version: 522.0.0.0.0
      OS Loader Version: 540.120.3~37
      SMC Version (system): 2.33f12

Software:

    System Software Overview:

      System Version: macOS 12.7.1 (21G920)
      Kernel Version: Darwin 21.6.0
      Time since boot: 43 days 6:00

Graphics/Displays:

    AMD Radeon R9 M380:

      Chipset Model: AMD Radeon R9 M380
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 2 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6640
      Revision ID: 0x0080
      ROM Revision: 113-C6005R-800
      VBIOS Version: 113-C6005T-009
      EFI Driver Version: 01.00.800
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL P4317Q:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: N6YFD77S017L
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort
          Television: Yes


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58
    ChimeraX-AtomicLibrary: 14.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.3
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.4
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9.dev202405110020
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.1
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.4
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 1.3.3
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.51.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.1
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.2
    typing-extensions: 4.11.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10

Change History (3)

comment:1 by Eric Pettersen, 15 months ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in garbage collection

comment:2 by Eric Pettersen, 15 months ago

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

Hi Peter,

Thanks for reporting this problem. The crash occurred in "garbage collection", where Python frees up the memory of objects it is no longer using, and therefore isn't necessarily directly related to the PAE coloring. Garbage collection problems are difficult to track down, but nonetheless every bug report gives us additional clues as to where the actual problem might be, so thanks for sending this.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by Tom Goddard, 15 months ago

Log shows using alphafold pae, coulombic, and contacts commands and closing the models a few times. Past garbage collection crashes were reproduced with coulombic and close so maybe those are the most probable places where something got corrupted.

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