Opened 3 months ago

Closed 3 months ago

Last modified 3 months ago

#18225 closed defect (can't reproduce)

Crash in event loop in QDockWidget::event

Reported by: chimerax-bug-report@… 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-15.5-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x0000000355807000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000316a73000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000315a67000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000314a5b000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000313a4f000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000312a43000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000311a37000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000310a2b000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030fa1f000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030ea13000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030da07000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030c9fb000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030b9ef000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030a9e3000 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x0000000208d41f00 (most recent call first):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.mlp._mlp, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw (total: 62)


{"app_name":"ChimeraX","timestamp":"2025-07-18 07:24:14.00 -0700","app_version":"1.10.0","slice_uuid":"9cf8124a-d876-34ad-b7ee-c011183ebc15","build_version":"1.10.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.5 (24F74)","roots_installed":0,"name":"ChimeraX","incident_id":"FCBA1807-2273-4A52-BBB9-3B31BCBB119B"}
{
  "uptime" : 510000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac16,10",
  "coalitionID" : 12052,
  "osVersion" : {
    "train" : "macOS 15.5",
    "build" : "24F74",
    "releaseType" : "User"
  },
  "captureTime" : "2025-07-18 07:23:56.7933 -0700",
  "codeSigningMonitor" : 2,
  "incident" : "FCBA1807-2273-4A52-BBB9-3B31BCBB119B",
  "pid" : 32810,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-07-18 06:53:33.4943 -0700",
  "procStartAbsTime" : 12275616264570,
  "procExitAbsTime" : 12319374514459,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"56DA4C97-9B61-5C46-843A-6F949204A539","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "988BD579-805F-87A2-B0C7-A921D95CBFAB",
  "appleIntelligenceStatus" : {"reasons":["siriAssetIsNotReady","notOptedIn","assetIsNotReady"],"state":"unavailable"},
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "9EE72B8E-B4E3-4EB0-8872-1E3B339A2012",
  "wakeTime" : 279347,
  "sleepWakeUUID" : "4C8210E0-9C87-411A-A25E-518A561E7B85",
  "sip" : "enabled",
  "vmRegionInfo" : "0x40 is not in any region.  Bytes before following region: 4366991296\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      1044b0000-1044b4000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000040","rawCodes":[1,64],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000040"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":32810},
  "vmregioninfo" : "0x40 is not in any region.  Bytes before following region: 4366991296\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      1044b0000-1044b4000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
  "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" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":5503220376},{"value":99},{"value":111},{"value":0},{"value":0},{"value":6294194721401617533},{"value":6294194730131268477},{"value":14757395258967641293},{"value":4294967286},{"value":5503220306},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8755158952},{"value":0},{"value":11},{"value":259},{"value":8738054112,"symbolLocation":224,"symbol":"_main_thread"},{"value":316},{"value":1},{"value":4387702320,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":1},{"value":6099881536},{"value":5216375872},{"value":6099883056}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6891448460},"cpsr":{"value":1073741824},"fp":{"value":5503220448},"sp":{"value":5503220416},"esr":{"value":1442840704,"description":" Address size 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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: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/sasmitapanda/Documents/SasmitaCopy/Sasmita/ITQB NOVA/LytH-PlsC
> Project/LytH-PlsC structures/LytH interaction.cxs"

> view name session-start

opened ChimeraX session  

> style sphere

Changed 1820 atom styles  

> mlp

Map values for surface "fold_2025_01_15_15_06_model_0.cif_A SES surface":
minimum -26.17, mean 3.089, maximum 22.17  
Map values for surface "fold_2025_01_15_15_06_model_0.cif_B SES surface":
minimum -25.83, mean -2.994, maximum 22.25  
To also show corresponding color key, enter the above mlp command and add key
true  

> rainbow

> mlp

Map values for surface "fold_2025_01_15_15_06_model_0.cif_A SES surface":
minimum -26.17, mean 3.089, maximum 22.17  
Map values for surface "fold_2025_01_15_15_06_model_0.cif_B SES surface":
minimum -25.83, mean -2.994, maximum 22.25  
To also show corresponding color key, enter the above mlp command and add key
true  

> select /B:2-16,25-27,44-52,64-67,70-79,91-102,117-134,149-152,176-204

833 atoms, 836 bonds, 104 residues, 1 model selected  

> close session

> open "/Users/sasmitapanda/Documents/SasmitaCopy/Sasmita/ITQB NOVA/LytH-PlsC
> Project/LytH-PlsC structures/LytH interaction.cxs" format session

> view name session-start

opened ChimeraX session  

> mlp

Map values for surface "fold_2025_01_15_15_06_model_0.cif_A SES surface":
minimum -26.17, mean 3.089, maximum 22.17  
Map values for surface "fold_2025_01_15_15_06_model_0.cif_B SES surface":
minimum -25.83, mean -2.994, maximum 22.25  
To also show corresponding color key, enter the above mlp command and add key
true  

> style stick

Changed 1820 atom styles  

> select /A

197 atoms, 200 bonds, 24 residues, 1 model selected  

> rainbow sel

> style sel stick

Changed 197 atom styles  

> style sel stick

Changed 197 atom styles  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> show sel cartoons

> mlp sel

Map values for surface "fold_2025_01_15_15_06_model_0.cif_A SES surface":
minimum -26.17, mean 3.089, maximum 22.17  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp sel

Map values for surface "fold_2025_01_15_15_06_model_0.cif_A SES surface":
minimum -26.17, mean 3.089, maximum 22.17  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp sel

Map values for surface "fold_2025_01_15_15_06_model_0.cif_A SES surface":
minimum -26.17, mean 3.089, maximum 22.17  
To also show corresponding color key, enter the above mlp command and add key
true  

> show sel cartoons

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> close session

> open "/Users/sasmitapanda/Documents/SasmitaCopy/Sasmita/ITQB NOVA/LytH-PlsC
> Project/LytH-PlsC structures/LytH interaction.cxs" format session

> view name session-start

opened ChimeraX session  

> select /B:2-16,25-27,44-52,64-67,70-79,91-102,117-134,149-152,176-204

833 atoms, 836 bonds, 104 residues, 1 model selected  

> select /B:205

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /B

1623 atoms, 1655 bonds, 205 residues, 1 model selected  

> mlp sel

Map values for surface "fold_2025_01_15_15_06_model_0.cif_B SES surface":
minimum -25.83, mean -2.994, maximum 22.25  
To also show corresponding color key, enter the above mlp command and add key
true  

> open Q2G1S7 fromDatabase uniprot format uniprot

Summary of feedback from opening Q2G1S7 fetched from uniprot  
---  
notes | Fetching compressed Q2G1S7 UniProt info from https://www.uniprot.org/uniprot/Q2G1S7.xml  
Alignment identifier is Q2G1S7  
  
Opened UniProt Q2G1S7  

> cartoon (#!1 & sel)

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> Open Q2G1S7

Unknown command: Open Q2G1S7  

> Open Q2G1S7 from uniprot

Unknown command: Open Q2G1S7 from uniprot  

> open 30495 fromDatabase emdb

Summary of feedback from opening 30495 fetched from emdb  
---  
notes | Fetching compressed map 30495 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-30495/map/emd_30495.map.gz  
Fetching map header 30495 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-30495/header/emd-30495.xml  
  
Opened emdb 30495 as #2, grid size 220,220,220, pixel 1.09, shown at level
0.7, step 1, values float32, fit PDB 7cxr  

> open Q2G1S7 fromDatabase uniprot

Summary of feedback from opening Q2G1S7 fetched from uniprot  
---  
notes | Destroying pre-existing alignment with identifier Q2G1S7  
Alignment identifier is Q2G1S7  
  
Opened UniProt Q2G1S7  

> ~select

Nothing selected  

> show surfaces

> hide #!1 models

> hide #!2 models

> select clear

> ui tool show AlphaFold

> alphafold match
> MFSTLFHVTKRTTRDYKYQLFPQVLLVFLLFIDTLHFHLSNTKKKLSNLCCLTPLYYPYFTIIHISLNYLMLASIFSIFLPSMTSLMRFVCNFLLSSNV

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold A0A7U9J3Z9 from
https://alphafold.ebi.ac.uk/files/AF-A0A7U9J3Z9-F1-model_v4.cif  
1 AlphaFold model found using sequence similarity searches: A0A7U9J3Z9 (1
sequences)  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
A0A7U9J3Z9_STAAU | MFSTL...LSSNV | 100.0 | 100.0    
Associated AlphaFold A0A7U9J3Z9_STAAU chain A to Q2G1S7 with 0 mismatches  
Opened 1 AlphaFold model  
> view clip false> open Q2FZ95 fromDatabase uniprot | Summary of feedback from opening Q2FZ95 fetched from uniprot  
---  
notes | Fetching compressed Q2FZ95 UniProt info from https://www.uniprot.org/uniprot/Q2FZ95.xml  
Alignment identifier is Q2FZ95  
  
Opened UniProt Q2FZ95  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> alphafold match
> MFSTLFHVTKRTTRDYKYQLFPQVLLVFLLFIDTLHFHLSNTKKKLSNLCCLTPLYYPYFTIIHISLNYLMLASIFSIFLPSMTSLMRFVCNFLLSSNV

1 AlphaFold model found using sequence similarity searches: A0A7U9J3Z9 (1
sequences)  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
A0A7U9J3Z9_STAAU | MFSTL...LSSNV | 100.0 | 100.0    
Associated AlphaFold A0A7U9J3Z9_STAAU chain A to Q2G1S7 with 0 mismatches  
Opened 1 AlphaFold model  
> show target m> hide #!1 models> hide #!2 models> show target m> hide #!1
> models> hide #!2 models> mlp #3-4Map values for surface "AlphaFold
> A0A7U9J3Z9_STAAU_A SES surface": minimum -27.04, mean 1.121, maximum 22.75  
To also show corresponding color key, enter the above mlp command and add key
true  
> undo> hide #!2 models> hide #!4 models> mlp #!3Map values for surface
> "AlphaFold A0A7U9J3Z9_STAAU_A SES surface": minimum -27.04, mean 1.121,
> maximum 22.75  
To also show corresponding color key, enter the above mlp command and add key
true  
> hide #!3 cartoons> hide #!3 surfaces> show #!3 surfaces> show #!3 cartoons>
> alphafold match
> MFSTLFHVTKRTTRDYKYQLFPQVLLVFLLFIDTLHFHLSNTKKKLSNLCCLTPLYYPYFTIIHISLNYLMLASIFSIFLPSMTSLMRFVCNFLLSSNV1
> AlphaFold model found using sequence similarity searches: A0A7U9J3Z9 (1
> sequences)  
| Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
A0A7U9J3Z9_STAAU | MFSTL...LSSNV | 100.0 | 100.0    
Associated AlphaFold A0A7U9J3Z9_STAAU chain A to Q2G1S7 with 0 mismatches  
Opened 1 AlphaFold model  
> view clip false> hide #!3 models> hide #5 models> show #!3 models> show #!4
> models> hide #!3 models> show #!3 models> hide #!4 models> hide #!3 models>
> show #5 models> alphafold match
> MAVEKVYQPYDEQVYNSIPKQQPQTKPEKKTVSRKVVVQLTKFEKVLYITLITVIAMLSIYMLSLKMDAYDTRGKIADLDYKIDKQSSENSALQSEIKKNSSYERIYEKAKKQGMSLENDNVKVVRSNGEAKNFetching
> compressed AlphaFold A0A0E0VP17 from
> https://alphafold.ebi.ac.uk/files/AF-A0A0E0VP17-F1-model_v4.cif  
1 AlphaFold model found using sequence similarity searches: A0A0E0VP17 (1
sequences)  
| Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
A0A0E0VP17_STAA5 | MAVEK...GEAKN | 100.0 | 100.0    
Associated AlphaFold A0A0E0VP17_STAA5 chain A to Q2FZ95 with 0 mismatches  
Opened 1 AlphaFold model  
> show #!1 models> close > open /Users/sasmitapanda/Downloads/ChimeraX/AlphaFold/AF-A0A0E0VP17-F1-model_v4.cif format mmcif | Chain information for AF-A0A0E0VP17-F1-model_v4.cif #1  
---  
Chain | Description | UniProt  
A | Cell division protein FtsL | A0A0E0VP17_STAA5 1-133  
  
Color AF-A0A0E0VP17-F1-model_v4.cif by residue attribute pLDDT_score  
Associated AF-A0A0E0VP17-F1-model_v4.cif chain A to Q2FZ95 with 0 mismatches  

> alphafold match
> MAVEKVYQPYDEQVYNSIPKQQPQTKPEKKTVSRKVVVQLTKFEKVLYITLITVIAMLSIYMLSLKMDAYDTRGKIADLDYKIDKQSSENSALQSEIKKNSSYERIYEKAKKQGMSLENDNVKVVRSNGEAKN

1 AlphaFold model found using sequence similarity searches: A0A0E0VP17 (1
sequences)  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
A0A0E0VP17_STAA5 | MAVEK...GEAKN | 100.0 | 100.0    
Associated AlphaFold A0A0E0VP17_STAA5 chain A to Q2FZ95 with 0 mismatches  
Opened 1 AlphaFold model  
> show target m> select clear> ui tool show AlphaFold


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

Log:
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac mini
      Model Identifier: Mac16,10
      Model Number: MU9E3YP/A
      Chip: Apple M4
      Total Number of Cores: 10 (4 performance and 6 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 8 days, 2 hours, 13 minutes

Graphics/Displays:

    Apple M4:

      Chipset Model: Apple M4
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        MP59G:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.5.0
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    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: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

Change History (3)

comment:1 by Eric Pettersen, 3 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 event loop

comment:2 by Eric Pettersen, 3 months ago

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

Was showing AlphaFold tool at the time

comment:3 by Tom Goddard, 3 months ago

Summary: Crash in event loop → Crash in event loop in QDockWidget::event

Was in QGuiApplicationPrivate::processMouseEvent() and QDockWidget::event().

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