Opened 21 months ago

Closed 21 months ago

#14409 closed defect (can't reproduce)

Crash in garbage collection while showing alignment

Reported by: chimerax-bug-report@… Owned by: pett
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-14.0-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000000031e0c0000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031d0bd000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031c0ba000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031a0b4000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031b0b7000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x0000000205059240 (most recent call first):
  Garbage-collecting
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/_internal.py", line 255 in __init__
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 333 in pointer
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 251 in set_cvec_pointer
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 133 in __init__
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 807 in __init__
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 73 in _non_null_atoms
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 209 in get_prop
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1933 in _colorize_label
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 2294 in _layout_line
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 2334 in layout_lines
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1638 in __init__
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1643 in __init__
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1643 in __init__
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1643 in __init__
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1643 in __init__
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1643 in __init__
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1643 in __init__
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1643 in __init__
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1643 in __init__
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 783 in layout_alignment
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 205 in __init__
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/tool.py", line 167 in _finalize_init
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/tool.py", line 55 in __init__
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/tool.py", line 928 in _start_seq_viewer
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/__init__.py", line 48 in run_provider
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/manager.py", line 258 in new_alignment
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 241 in seqalign_chain
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/show_sequences/tool.py", line 77 in show_seqs
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, lxml._elementpath, lxml.etree, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, 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, chimerax.mmcif.mmcif_write (total: 55)


{"app_name":"ChimeraX","timestamp":"2024-01-18 16:33:36.00 -0800","app_version":"1.7.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.7.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.0 (23A344)","roots_installed":0,"name":"ChimeraX","incident_id":"3E52437D-A732-4319-B24E-D3D697E648C9"}
{
  "uptime" : 15000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac14,2",
  "coalitionID" : 1859,
  "osVersion" : {
    "train" : "macOS 14.0",
    "build" : "23A344",
    "releaseType" : "User"
  },
  "captureTime" : "2024-01-18 16:33:32.5112 -0800",
  "codeSigningMonitor" : 1,
  "incident" : "3E52437D-A732-4319-B24E-D3D697E648C9",
  "pid" : 4673,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-01-18 15:48:59.2031 -0800",
  "procStartAbsTime" : 312954768309,
  "procExitAbsTime" : 377111971962,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"DC33E73C-FA52-5625-BB1C-E16B2534C308","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "D90B7D68-427E-98ED-CD16-515C91CC8B65",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "wakeTime" : 8026,
  "sleepWakeUUID" : "C76EFC1E-A370-4B4F-8CFD-2EA3ABD300C9",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 140722823462743\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffc95e78000-7ffcbb598000 [599.1M] r-x\/r-x SM=COW  ...t_id=b581fab3",
  "exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":4673},
  "ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 140722823462743\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffc95e78000-7ffcbb598000 [599.1M] r-x\/r-x SM=COW  ...t_id=b581fab3",
  "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,
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    "arch" : "x86_64",
    "base" : 140703332319232,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 2736117,
    "uuid" : "ad043d3b-2199-381b-96f2-2d827bae0c57",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703206658048,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 20979712,
    "uuid" : "70a55260-7bb1-3c07-aac3-402d42fa9913",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2487"
  }
],
  "sharedCache" : {
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  "size" : 21474836480,
  "uuid" : "fb8ba21b-013a-3f11-b51e-5d5b4271240d"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=2.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.2G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               128K        1 \nActivity Tracing                   256K        1 \nCG image                           208K       20 \nColorSync                          240K       30 \nCoreAnimation                     4220K      101 \nCoreGraphics                        32K        5 \nCoreUI image data                 4628K       34 \nDispatch continuations            64.0M        1 \nFoundation                          36K        2 \nKernel Alloc Once                    8K        1 \nMALLOC                             1.2G      255 \nMALLOC guard page                  384K       24 \nMach message                        16K        4 \nOpenGL GLSL                        384K        4 \nRosetta Arena                     4096K        2 \nRosetta Generic                   1676K      416 \nRosetta IndirectBranch            2048K        1 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack               836K       82 \nRosetta Thread Context             820K       82 \nSTACK GUARD                         40K       10 \nStack                            241.6M       43 \nStack Guard                       56.1M       33 \nVM_ALLOCATE                      254.8M      339 \nVM_ALLOCATE (reserved)           128.1M       11         reserved VM address space (unallocated)\n__CTF                               824        1 \n__DATA                            56.3M      827 \n__DATA_CONST                      48.2M      451 \n__DATA_DIRTY                      1863K      237 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       170.3M      156 \n__OBJC_RO                         70.5M        1 \n__OBJC_RW                         2151K        2 \n__TEXT                             1.0G      833 \ndyld private memory                420K        4 \nmapped file                        7.3G     1542 \nshared memory                     3008K       25 \nunshared pmap                     15.0M        9 \n===========                     =======  ======= \nTOTAL                             10.7G     5594 \nTOTAL, minus reserved VM space    10.6G     5594 \n",
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},
  "logWritingSignature" : "7764fe3580b277bc4513c5e298daf0313b832218",
  "trialInfo" : {
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  "experiments" : [

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},
  "reportNotes" : [
  "PC register does not match crashing frame (0x0 vs 0x7FF89181AA78)"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/TO SAVE DATA
> W3/cryosparc_P3_J171_006_volume_map_sym_sharp.mrc" format mrc

Opened cryosparc_P3_J171_006_volume_map_sym_sharp.mrc as #1, grid size
448,448,448, pixel 0.86, shown at level 0.894, step 2, values float32  

> open /Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly.cif

Summary of feedback from opening
/Users/yiyingli/Library/CloudStorage/OneDrive-
UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly.cif  
---  
warnings | Unknown polymer entity '1' near line 342  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for fresh_group1_assembly.cif #2  
---  
Chain | Description  
K M O Q S U W Y a c e g i k m o q s u | No description available  
  

> hide atoms

> show cartoons

> hide #!1 models

> ui tool show "Change Chain IDs"

> changechains 2 1

Chain IDs of 68 residues changed  

> open formats

Command Script  
---  
File format| Short name(s)| Suffixes  
ChimeraX commands| cmd| .cxc  
Compiled Python code| compiled python| .pyc, .pyo  
Python code| python| .py  
  
Documentation  
---  
File format| Short name(s)| Suffixes  
HTML| html| .html, .htm, .xhtml, .xht, .xml  
  
Generic 3D Objects  
---  
File format| Short name(s)| Suffixes  
Chimera BILD object| bild| .bild, .bld  
COLLADA| collada| .dae  
Direction dependent resolution values| fsc| .dres  
glTF| gltf| .glb  
Interatomic pseudobonds| pseudobonds| .pb  
Marker model| markers| .cmm  
Model Positions| positions| .positions  
Mole tunnels| mole| .json  
NMR-STAR distance restraints*| nmrstr| .str  
STL (3D printing)| stl| .stl  
STORM microscopy| storm| .storm  
SWC neuron traces| swc| .swc  
VTK PolyData| vtk| .vtk  
Wavefront OBJ| obj| .obj  
*Not installed; click on link to install  
  
Geometric Model  
---  
File format| Short name(s)| Suffixes  
ArtiaX geometric model*| geomodel| .axm  
*Not installed; click on link to install  
  
Higher-Order Structure  
---  
File format| Short name(s)| Suffixes  
Integrative/Hybrid Models| ihm| .ihm  
  
Image  
---  
File format| Short name(s)| Suffixes  
photo| photo| .jpg  
  
Medical Imaging  
---  
File format| Short name(s)| Suffixes  
DICOM| dicom| .dcm  
  
Molecular Structure  
---  
File format| Short name(s)| Suffixes  
Amber SQM output file*| sqmout| .sqmout  
AutoDock PDBQT| pdbqt| .pdbqt  
Formatted Checkpoint file*| fchk| .fchk  
Gaussian input file*| com| .com, .gjf  
Gaussian output file*| log| .log  
Gromos87 structure| gro| .gro  
Macromolecular Transmission| mmtf| .mmtf  
Maestro| schrodinger maestro| .mae, .maegz  
mmCIF| mmcif| .cif, .mmcif  
MOL/SDF| sdf| .sdf, .mol  
Mol2| mol2| .mol2  
NBO input file*| nbo47| .47  
NBO output file*| nbo31| .31  
ORCA output file*| out| .out  
PDB| pdb| .pdb, .pdb1, .ent, .pqr  
PSF| psf| .psf  
Psi4 output file*| dat| .dat, .out  
Q-Chem output file*| qout| .qout, .out, .dat  
RMF*| rmf| .rmf, .rmf3  
Small Molecule CIF| corecif or smallcif| .cif  
SwissDock| swissdock| .pdb  
VIPERdb| viperdb| .vdb  
XYZ coordinate file*| xyz| .xyz  
ZDOCK| zdock| .pdb  
*Not installed; click on link to install  
  
Molecular Trajectory  
---  
File format| Short name(s)| Suffixes  
Amber netCDF format| amber| .nc  
DCD trajectory format| dcd| .dcd  
Gromacs trr format| trr| .trr  
Gromacs xtc format| xtc| .xtc  
XYZ trajectory file*| allxyz| .allxyz  
*Not installed; click on link to install  
  
Particle List  
---  
File format| Short name(s)| Suffixes  
Artiatomi particle lists*| motl or motivelist| .em  
Dynamo particle table*| dynamo or tbl| .tbl  
IMOD model2point output*| coords or model2point| .coords  
PEET model/csv*| peet| .mod  
RELION star files*| star or relion| .star  
TSV particle lists*| generic_particles| .tsv  
*Not installed; click on link to install  
  
Sequence  
---  
File format| Short name(s)| Suffixes  
Clustal ALN sequence| aln or clustal| .aln, .clustal, .clustalw, .clustalx  
FASTA sequence| fasta| .fa, .fasta, .afasta, .afa  
HSSP sequence| hssp| .hssp  
MSF sequence| msf| .msf  
Pfam sequence| pfam| .selex, .slx, .pfam  
PIR sequence| pir| .ali, .pir  
RSF sequence| rsf| .rsf  
Stockholm sequence| stockholm| .sth, .sto  
  
Session  
---  
File format| Short name(s)| Suffixes  
ChimeraX session| session| .cxs  
  
Structure Analysis  
---  
File format| Short name(s)| Suffixes  
Attributes| defattr| .defattr  
  
Structure Factors  
---  
File format| Short name(s)| Suffixes  
MTZ*| mtz| .mtz  
*Not installed; click on link to install  
  
Volume Data  
---  
File format| Short name(s)| Suffixes  
Amira mesh| amira| .am  
APBS potential| apbs| .dx  
BRIX density map| brix| .brix  
CCP4 density map| ccp4| .ccp4, .map  
Chimera map| cmap| .cmap, .cmp  
CNS or XPLOR density map| xplor| .cns, .xplor  
DelPhi or GRASP potential| delphi| .phi  
DeltaVision map| dv| .dv  
DOCK scoring grid| dock| .bmp, .cnt, .nrg  
DSN6 density map| dsn6| .omap  
EMAN HDF map| emanhdf| .hdf, .hdf5, .h5  
EMDB SFF| sff| .sff, .hff  
Gaussian cube grid| cube| .cube, .cub  
gOpenMol grid| gopenmol| .plt  
HDF map| hdf|  
Image stack| images| .tif, .tiff, .png, .pgm  
IMAGIC density map| imagic| .hed, .img  
Imaris map| ims| .ims  
IMOD map| imodmap| .rec  
IMOD model| imod| .imod, .mod  
MacMolPlt grid| macmolplt| .mmp  
MRC density map| mrc| .mrc  
NetCDF map| netcdfmap| .nc  
NIfTI| nifti| .nii, .nii.gz  
NRRD| nrrd| .nrrd  
Priism microscope image| priism| .xyzw, .xyzt  
PROFEC free energy grid| profec| .profec  
Purdue image format| pif| .pif  
Segger segmentation| segger| .seg  
SITUS map file| situs| .sit, .situs  
SPIDER volume data| spider| .spi, .vol  
TOM toolbox EM density map| tom_em| .em  
UHBD grid, binary| uhbd| .grd  
  
Database| Formats  
---|---  
alphafold| mmcif  
ccd| ccd  
cellpack| cellpack  
cod| cod  
eds| ccp4  
edsdiff| ccp4  
emdb| ccp4  
emdb_china| ccp4  
emdb_europe| ccp4  
emdb_fits| ccp4  
emdb_japan| ccp4  
emdb_us| ccp4  
esmfold| pdb  
iupac| iupac  
pcod| pcod  
pdb| mmcif, mmtf, pdb  
pdb_nmr| nmrstr  
pdbdev| ihm  
pdbe| mmcif, pdb  
pdbe_bio| mmcif  
pdbj| mmcif, pdb  
pubchem| sdf  
rcsb_bio| mmcif  
smiles| smiles  
uniprot| uniprot  
  

> log metadata #2

No models had metadata

> log chains #2

Chain information for fresh_group1_assembly.cif #2  
---  
Chain | Description  
K M O Q S U W Y a c e g i k m o q s u | No description available  
  

> select /K:156-605

3131 atoms, 3173 bonds, 403 residues, 1 model selected  

> show #!1 models

> hide #!1 models

> changechains #2/K A

Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (A/800/)  

> select ::name="HOH"

2040 atoms, 2040 residues, 1 model selected  

> delete sel

> show #!1 models

> view orient

> save /Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly2.cif relModel
> #2

Not saving entity_poly_seq for non-authoritative sequences  

> open /Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly2.cif

Summary of feedback from opening
/Users/yiyingli/Library/CloudStorage/OneDrive-
UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly2.cif  
---  
warnings | Unknown polymer entity '1' near line 281  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for fresh_group1_assembly2.cif #3  
---  
Chain | Description  
K M O Q S U W Y a c e g i k m o q s u | No description available  
  

> hide #!2 models

> hide atoms

> show cartoons

> volume #1 level 2

> volume #1 step 1

> hide #!3 models

> close #2

> log metadata #3

No models had metadata

> log chains #3

Chain information for fresh_group1_assembly2.cif #3  
---  
Chain | Description  
K M O Q S U W Y a c e g i k m o q s u | No description available  
  

> open "/Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM
> final/ATP_C1_class1/helix_ATP_C1_refined.pdb"

Summary of feedback from opening
/Users/yiyingli/Library/CloudStorage/OneDrive-
UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM
final/ATP_C1_class1/helix_ATP_C1_refined.pdb  
---  
warnings | Ignored bad PDB record found on line 20  
  
  
Ignored bad PDB record found on line 21  
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2  
  
Ignored bad PDB record found on line 22  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 23  
BOND : 0.007 0.097 96540  
  
Ignored bad PDB record found on line 24  
ANGLE : 0.891 19.396 130620  
  
18 messages similar to the above omitted  
  
Chain information for helix_ATP_C1_refined.pdb #2  
---  
Chain | Description  
1 3 5 7 A C E G I K M O Q S U W Y a c e g i k m o q s u w y | No description
available  
  

> close #2

> log metadata #3

No models had metadata

> log chains #3

Chain information for fresh_group1_assembly2.cif #3  
---  
Chain | Description  
K M O Q S U W Y a c e g i k m o q s u | No description available  
  

> open /Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly_rename.cif

Summary of feedback from opening
/Users/yiyingli/Library/CloudStorage/OneDrive-
UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly_rename.cif  
---  
warning | Unknown polymer entity '1' near line 27  
  

> log metadata #3

No models had metadata

> log chains #3

Chain information for fresh_group1_assembly2.cif #3  
---  
Chain | Description  
K M O Q S U W Y a c e g i k m o q s u | No description available  
  

> log metadata #2

The model has no metadata

> log chains #2

> hide #2 models

> show #2 models

> open /Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly_rename2.cif

Summary of feedback from opening
/Users/yiyingli/Library/CloudStorage/OneDrive-
UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly_rename2.cif  
---  
warning | Unknown polymer entity '1' near line 27  
  

> log metadata #4

The model has no metadata

> log chains #4

> open /Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly3.cif

Summary of feedback from opening
/Users/yiyingli/Library/CloudStorage/OneDrive-
UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly3.cif  
---  
warning | Unknown polymer entity '1' near line 27  
  

> close #4

> close #2

> close #5

> log metadata #3

No models had metadata

> log chains #3

Chain information for fresh_group1_assembly2.cif #3  
---  
Chain | Description  
K M O Q S U W Y a c e g i k m o q s u | No description available  
  

> select /K:156-605

3131 atoms, 3173 bonds, 403 residues, 1 model selected  

> show #!3 models

> open /Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly3.cif

Summary of feedback from opening
/Users/yiyingli/Library/CloudStorage/OneDrive-
UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/fresh_group1_assembly3.cif  
---  
warning | Unknown polymer entity '1' near line 27  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #3/K

Alignment identifier is 3/K  

> sequence chain #3/M

Alignment identifier is 3/M  

> sequence chain #3/O

Alignment identifier is 3/O  

> sequence chain #3/Q

Alignment identifier is 3/Q  

> sequence chain #3/S

Alignment identifier is 3/S  

> sequence chain #3/U

Alignment identifier is 3/U  


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

Log:
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac
      Model Identifier: Mac14,2
      Model Number: FLY13LL/A
      Chip: Unknown
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 10151.1.1
      OS Loader Version: 10151.1.1

Software:

    System Software Overview:

      System Version: macOS 14.0 (23A344)
      Kernel Version: Darwin 23.0.0
      Time since boot: 21 hours, 14 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2414H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 50.00Hz
          Mirror: Off
          Online: Yes


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    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: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    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: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    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: 1.4
    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: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    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-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    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: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    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: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by pett, 21 months ago

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

comment:2 by pett, 21 months ago

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