Opened 5 weeks ago

Closed 5 weeks ago

#19025 closed defect (can't reproduce)

Crash drawing graphics after resize

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-26.0.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error

Thread 0x000000030704f000 (most recent call first):
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000306043000 (most recent call first):
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000305037000 (most recent call first):
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030402b000 (most recent call first):
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030301f000 (most recent call first):
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000302013000 (most recent call first):
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000301007000 (most recent call first):
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000017f423000 (most recent call first):
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000017e417000 (most recent call first):
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000017d40b000 (most recent call first):
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000017c3ff000 (most recent call first):
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000017b3f3000 (most recent call first):
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000017a3e7000 (most recent call first):
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001ee390800 (most recent call first):
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 166 in status
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 98 in _expose_event
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 122 in make_current
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 555 in make_current
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 584 in use_shared_context
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 143 in render
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 113 in _redraw
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 100 in draw_new_frame
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 169 in update_graphics_now
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 153 in resizeEvent
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 61 in event
  File "/Applications/ChimeraX-1.10.1.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-1.10.1.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-1.10.1.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.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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, PIL._imaging, PIL._imagingmath, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 53)


{"app_name":"ChimeraX","timestamp":"2025-10-04 13:30:53.00 +0800","app_version":"1.10.1","slice_uuid":"9cf8124a-d876-34ad-b7ee-c011183ebc15","build_version":"1.10.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.0.1 (25A362)","roots_installed":0,"name":"ChimeraX","incident_id":"140F4272-AA50-43AC-9427-197CE096AA79"}
{
  "uptime" : 9300,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac16,10",
  "coalitionID" : 2017,
  "osVersion" : {
    "train" : "macOS 26.0.1",
    "build" : "25A362",
    "releaseType" : "User"
  },
  "captureTime" : "2025-10-04 13:30:31.7908 +0800",
  "codeSigningMonitor" : 2,
  "incident" : "140F4272-AA50-43AC-9427-197CE096AA79",
  "pid" : 2332,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-10-04 11:12:12.5514 +0800",
  "procStartAbsTime" : 127741325519,
  "procExitAbsTime" : 225170525347,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.10.1","CFBundleVersion":"1.10.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"469EA8D9-2583-58C7-825C-CC7AAE997969","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "DA9147E2-3DEF-1C21-A127-E257534A894F",
  "developerMode" : 1,
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "82743210-B1D5-4707-AC84-63CEB445211B",
  "wakeTime" : 2,
  "sleepWakeUUID" : "74374F51-ECE4-4B89-9E3E-91EBBCA8D231",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa00001300 is in 0x78e000000-0xa80c00000;  bytes after start: 10502542080  bytes before end: 2160061695\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      MALLOC_LARGE                70ac00000-70b000000    [ 4096K] rw-\/rwx SM=PRV  \n      GAP OF 0x83000000 BYTES\n--->  commpage (reserved)         78e000000-a80c00000    [ 11.8G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n      MALLOC_SMALL                a80c00000-a81000000    [ 4096K] rw-\/rwx SM=PRV  ",
  "exception" : {"codes":"0x0000000000000002, 0x0000000a00001300","rawCodes":[2,42949677824],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000a00001300"},
  "termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":2332},
  "vmregioninfo" : "0xa00001300 is in 0x78e000000-0xa80c00000;  bytes after start: 10502542080  bytes before end: 2160061695\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      MALLOC_LARGE                70ac00000-70b000000    [ 4096K] rw-\/rwx SM=PRV  \n      GAP OF 0x83000000 BYTES\n--->  commpage (reserved)         78e000000-a80c00000    [ 11.8G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n      MALLOC_SMALL                a80c00000-a81000000    [ 4096K] rw-\/rwx SM=PRV  ",
  "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" : 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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: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:quickstart

> open
> /Users/ngimchandara/Downloads/single_record_question_GeneRecordClasses_GeneRecordClass.fasta

Summary of feedback from opening
/Users/ngimchandara/Downloads/single_record_question_GeneRecordClasses_GeneRecordClass.fasta  
---  
note | Alignment identifier is single_record_question_GeneRecordClasses_GeneRecordClass.fasta  
  
Opened 1 sequence from
single_record_question_GeneRecordClasses_GeneRecordClass.fasta  

> open
> /Users/ngimchandara/Downloads/single_record_question_GeneRecordClasses_GeneRecordClass.fasta
> format fasta

Summary of feedback from opening
/Users/ngimchandara/Downloads/single_record_question_GeneRecordClasses_GeneRecordClass.fasta  
---  
notes | Destroying pre-existing alignment with identifier single_record_question_GeneRecordClasses_GeneRecordClass.fasta  
Alignment identifier is
single_record_question_GeneRecordClasses_GeneRecordClass.fasta  
  
Opened 1 sequence from
single_record_question_GeneRecordClasses_GeneRecordClass.fasta  

> open Q8I434 fromDatabase uniprot format uniprot

Summary of feedback from opening Q8I434 fetched from uniprot  
---  
notes | Fetching compressed Q8I434 UniProt info from https://www.uniprot.org/uniprot/Q8I434.xml  
Alignment identifier is Q8I434  
  
Opened UniProt Q8I434  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> select clear

> ~select

Nothing selected  

> ui tool show "Blast Protein"

Cannot run BLAST without some kind of sequence. Please open a model and select
a chain, or input sequences or a UniProt ID.  

> help help:quickstart

> open 2bbv

Summary of feedback from opening 2bbv fetched from pdb  
---  
notes | Fetching compressed mmCIF 2bbv from http://files.rcsb.org/download/2bbv.cif  
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif  
  
2bbv title:  
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]  
  
Chain information for 2bbv #1  
---  
Chain | Description | UniProt  
A B C | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 1-363  
D E F | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 364-407  
N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') |   
  
Non-standard residues in 2bbv #1  
---  
CA — calcium ion  
  
2bbv mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  

> color bychain

> show surfaces

> show cartoons

> hide cartoons

> hide surfaces

> style sphere

Changed 7817 atom styles  

> style ball

Changed 7817 atom styles  

> color byhetero

> color bychain

> color bypolymer

> color bychain

> color bynucleotide

> color bfactor

7817 atoms, 1208 residues, 7 surfaces, atom bfactor range 0 to 59.2  

> nucleotides stubs

> ~hbonds

> show surfaces

> show cartoons

> show surfaces

> hide surfaces

> style sphere

Changed 7817 atom styles  

> lighting full

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> ui tool show "Side View"

> view

> volume step 2

No volumes specified  

> volume step 1

No volumes specified  

> volume style surface

No volumes specified  

> volume style mesh

No volumes specified  

> color bypolymer

> color bychain

> lighting simple

> hide target m

> close

> ui tool show "Show Sequence Viewer"

> open
> /Users/ngimchandara/Downloads/single_record_question_GeneRecordClasses_GeneRecordClass.fasta

Summary of feedback from opening
/Users/ngimchandara/Downloads/single_record_question_GeneRecordClasses_GeneRecordClass.fasta  
---  
note | Alignment identifier is single_record_question_GeneRecordClasses_GeneRecordClass.fasta  
  
Opened 1 sequence from
single_record_question_GeneRecordClasses_GeneRecordClass.fasta  

> open
> /Users/ngimchandara/Downloads/single_record_question_GeneRecordClasses_GeneRecordClass.fasta
> format fasta

Summary of feedback from opening
/Users/ngimchandara/Downloads/single_record_question_GeneRecordClasses_GeneRecordClass.fasta  
---  
notes | Destroying pre-existing alignment with identifier single_record_question_GeneRecordClasses_GeneRecordClass.fasta  
Alignment identifier is
single_record_question_GeneRecordClasses_GeneRecordClass.fasta  
  
Opened 1 sequence from
single_record_question_GeneRecordClasses_GeneRecordClass.fasta  

> open /Users/ngimchandara/Downloads/AF-Q8I434-F1-model_v4.pdb

AF-Q8I434-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for transcription factor 25, putative
(Q8I434) [more info...]  
  
Chain information for AF-Q8I434-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | transcription factor 25, putative | Q8I434_PLAF7 1-929  
  
Computing secondary structure  

> open /Users/ngimchandara/Downloads/AF-Q9BQ70-F1-model_v4.pdb

AF-Q9BQ70-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for transcription factor 25 (Q9BQ70) [more
info...]  
  
Chain information for AF-Q9BQ70-F1-model_v4.pdb #2  
---  
Chain | Description | UniProt  
A | transcription factor 25 | TCF25_HUMAN 1-676  
  
Computing secondary structure  

> matchmaker #1 and #2

Expected a keyword  

> matchmaker #1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-Q9BQ70-F1-model_v4.pdb, chain A (#2) with
AF-Q8I434-F1-model_v4.pdb, chain A (#1), sequence alignment score = 616  
RMSD between 204 pruned atom pairs is 1.046 angstroms; (across all 604 pairs:
33.527)  
  

> set bgColor white

> set bgColor #ffffff00

> set bgColor black

> set bgColor transparent

> open /Users/ngimchandara/Downloads/AF-S8G8F1-F1-model_v4.pdb

AF-S8G8F1-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for uncharacterized protein (S8G8F1) [more
info...]  
  
Chain information for AF-S8G8F1-F1-model_v4.pdb #3  
---  
Chain | Description | UniProt  
A | uncharacterized protein | S8G8F1_TOXGM 1-788  
  
Computing secondary structure  

> matchmaker #1 to #2 to #3

Repeated keyword argument "to"  

> matchmaker #1 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-S8G8F1-F1-model_v4.pdb, chain A (#3) with
AF-Q8I434-F1-model_v4.pdb, chain A (#1), sequence alignment score = 1056.8  
RMSD between 316 pruned atom pairs is 1.010 angstroms; (across all 714 pairs:
37.173)  
  

> hide #2 models

> matchmaker #1 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-S8G8F1-F1-model_v4.pdb, chain A (#3) with
AF-Q8I434-F1-model_v4.pdb, chain A (#1), sequence alignment score = 1056.8  
RMSD between 316 pruned atom pairs is 1.010 angstroms; (across all 714 pairs:
37.173)  
  

> matchmaker #1 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-S8G8F1-F1-model_v4.pdb, chain A (#3) with
AF-Q8I434-F1-model_v4.pdb, chain A (#1), sequence alignment score = 1056.8  
RMSD between 316 pruned atom pairs is 1.010 angstroms; (across all 714 pairs:
37.173)  
  

> show #2 models

> hide #2 models

> hide #1 models

> show #2 models

> hide #2 models

> show #1 models

> show #2 models

> hide #3 models

> hide #2 models

> show #2 models

> hide #2 models

> show #3 models

> hide #3 models

> open
> /Users/ngimchandara/Downloads/TCF25_942d6/TCF25_942d6_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb

Chain information for
TCF25_942d6_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb #4  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> view #4

> show target m

> hide target m

> show target m

> show #4 target m

> close #4

> hide #2 models

> hide #1 models

> hide #3 models

> open
> /Users/ngimchandara/Downloads/TCF25_942d6/TCF25_942d6_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb

Chain information for
TCF25_942d6_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb #4  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> matchmaker #1 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TCF25_942d6_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#4) with AF-Q8I434-F1-model_v4.pdb, chain A (#1), sequence alignment
score = 4582.6  
RMSD between 482 pruned atom pairs is 0.518 angstroms; (across all 929 pairs:
24.628)  
  

> show #4 target m

> show #1 target m

> open /Users/ngimchandara/Downloads/TCF25_942d6/config.json

Failed opening file /Users/ngimchandara/Downloads/TCF25_942d6/config.json:  
JSON file "/Users/ngimchandara/Downloads/TCF25_942d6/config.json" is not
AlphaFold predicted aligned error data, expected a top level list  

> open
> /Users/ngimchandara/Downloads/TCF25_942d6/TCF25_942d6_scores_rank_001_alphafold2_ptm_model_3_seed_000.json

Opened AlphaFold PAE with values for 929 residues and atoms  

> color #4/A:236-461 lime

> color #4/A:234 lime

> color #4/A:224 magenta

> color #4/A:225-525 lime

> color #4/A:349 lime

> color #4/A:132-136 magenta

> color #4/A:230-335 lime

> log metadata #1

Metadata for AF-Q8I434-F1-model_v4.pdb #1  
---  
Title | Alphafold monomer V2.0 prediction for transcription factor 25, putative (Q8I434)  
Source (natural) | Plasmodium falciparum (isolate 3D7)  
  
> log chains #1

Chain information for AF-Q8I434-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | transcription factor 25, putative | Q8I434_PLAF7 1-929  
  

> log metadata #2

Metadata for AF-Q9BQ70-F1-model_v4.pdb #2  
---  
Title | Alphafold monomer V2.0 prediction for transcription factor 25 (Q9BQ70)  
Source (natural) | Homo sapiens  
  
> log chains #2

Chain information for AF-Q9BQ70-F1-model_v4.pdb #2  
---  
Chain | Description | UniProt  
A | transcription factor 25 | TCF25_HUMAN 1-676  
  

> log metadata #3

Metadata for AF-S8G8F1-F1-model_v4.pdb #3  
---  
Title | Alphafold monomer V2.0 prediction for uncharacterized protein (S8G8F1)  
Source (natural) | Toxoplasma gondii (strain ATCC 50611 / ME49)  
  
> log chains #3

Chain information for AF-S8G8F1-F1-model_v4.pdb #3  
---  
Chain | Description | UniProt  
A | uncharacterized protein | S8G8F1_TOXGM 1-788  
  

> log metadata #4

The model has no metadata

> log chains #4

Chain information for
TCF25_942d6_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb #4  
---  
Chain | Description  
A | No description available  
  

> hide target m

> show target m

> hide target m

> show #4 target m

> color #4/A:928 lime

> color #4/A:48 magenta

> color #4/A:298-395 lime

> color #4/A:310-388 lime

> color #4/A:414-429 magenta

> color #4/A:312-314 lime

> color #4/A:630 magenta

> color #4/A:76-164 lime

> color #4/A:523-647 magenta

> color #4/A:111-181 lime

> color #4/A:397-580 magenta

> color #4/A:61 lime

> color #4/A:518 magenta

> color #4/A:57-165 lime

> color #4/A:177-403 magenta

> color #4/A:141 lime

> color #4/A:578 magenta

> color #4/A:333 lime

> color #4/A:66 magenta

> color #4/A:538-539 lime

> color #4/A:471 magenta

> color #4/A:489 lime

> color #4/A:495 magenta

> open
> /Users/ngimchandara/Downloads/TCF25_942d6/TCF25_942d6_scores_rank_002_alphafold2_ptm_model_4_seed_000.json

Opened AlphaFold PAE with values for 929 residues and atoms  

> color #4/A:217-379 lime

> color #4/A:373 lime

> color #4/A:387 magenta

> color bfactor #4 palette alphafold

7755 atoms, 929 residues, atom bfactor range 19.8 to 97  

> alphafold pae #4 colorDomains true

> color bfactor #4 palette alphafold

7755 atoms, 929 residues, atom bfactor range 19.8 to 97  

> alphafold pae #4 colorDomains true

> color bfactor #4 palette alphafold

7755 atoms, 929 residues, atom bfactor range 19.8 to 97  

> color bfactor #4 palette alphafold

7755 atoms, 929 residues, atom bfactor range 19.8 to 97  

> help help:user/tools/alphafold.html#pae

> color bfactor #4 palette alphafold

7755 atoms, 929 residues, atom bfactor range 19.8 to 97  

> color #4/A:641-724 lime

> color #4/A:506-527 magenta

> color #4/A:57-518 lime

> color #4/A:491 lime

> color #4/A:180-182 magenta

> color #4/A:125-150 lime

> color #4/A:285-287 lime

> color #4/A:149 magenta

> open
> /Users/ngimchandara/Downloads/TCF25_942d6/TCF25_942d6_scores_rank_003_alphafold2_ptm_model_5_seed_000.json

Opened AlphaFold PAE with values for 929 residues and atoms  

> color #4/A:106-377 lime

> color #4/A:318-319 lime

> color #4/A:433 magenta

> color #4/A:229-477 lime

> color #4/A:794 lime

> color #4/A:468 magenta

> open /Users/ngimchandara/Downloads/TCF25_942d6/config.json

Failed opening file /Users/ngimchandara/Downloads/TCF25_942d6/config.json:  
JSON file "/Users/ngimchandara/Downloads/TCF25_942d6/config.json" is not
AlphaFold predicted aligned error data, expected a top level list  

> open
> /Users/ngimchandara/Downloads/TCF25_942d6/TCF25_942d6_scores_rank_001_alphafold2_ptm_model_3_seed_000.json

Opened AlphaFold PAE with values for 929 residues and atoms  

> color #4/A:116-416 lime

> color #4/A:582-584 lime

> color #4/A:204-207 magenta

> open
> /Users/ngimchandara/Downloads/TCF25_942d6/TCF25_942d6_scores_rank_001_alphafold2_ptm_model_3_seed_000.json

Opened AlphaFold PAE with values for 929 residues and atoms  

> open
> /Users/ngimchandara/Downloads/TCF25_942d6/TCF25_942d6_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb

Chain information for
TCF25_942d6_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #5  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> hide #4 models

> show #1 models

> hide #1 models

> open
> /Users/ngimchandara/Downloads/TCF25_942d6/TCF25_942d6_scores_rank_001_alphafold2_ptm_model_3_seed_000.json

Failed opening file
/Users/ngimchandara/Downloads/TCF25_942d6/TCF25_942d6_scores_rank_001_alphafold2_ptm_model_3_seed_000.json:  
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command structure option, for example  
  
open
/Users/ngimchandara/Downloads/TCF25_942d6/TCF25_942d6_scores_rank_001_alphafold2_ptm_model_3_seed_000.json
structure #1  
  
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as  
  
open mole_channels.json format mole  


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

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 90.5
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: MU9D3CH/A
      Chip: Apple M4
      Total Number of Cores: 10 (4 performance and 6 efficiency)
      Memory: 16 GB
      System Firmware Version: 13822.1.2
      OS Loader Version: 13822.1.2

Software:

    System Software Overview:

      System Version: macOS 26.0.1 (25A362)
      Kernel Version: Darwin 25.0.0
      Time since boot: 3 hours, 48 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 4
      Displays:
        Mi Monitor:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 120.00Hz
          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
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    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: 14.1.19
    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: 1.10.1
    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: 1.1.3
    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: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    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: 4.3.2
    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
    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: 4.14.1
    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 (2)

comment:1 by Eric Pettersen, 5 weeks ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash drawing graphics after resize

comment:2 by Tom Goddard, 5 weeks ago

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

The Python stack trace shows a Qt ResizeEvent was dispatched which caused the graphics to redraw, and at the end of the graphics redraw the Side View got a trigger and made the QOpenGLContext current on the side view window, and within QOpenGLContext.makeCurrent() Qt dispatched an expose event on the status line which then made its own QOpenGLContext current and redrew the status line and then called swap buffers which crashed.

QOpenGLContext makeCurrent() dispatching an Qt expose event is sure to cause chaos. That is a a Qt bug. I didn't see any Qt bug report for it. I'm not 100% sure we can trust the Python traceback that shows this chain of function calls

chimerax/graphics/opengl.py", line 248 in swap_buffers
chimerax/graphics/opengl.py", line 561 in swap_buffers
chimerax/ui/statusbar.py", line 166 in status
chimerax/ui/statusbar.py", line 98 in _expose_event
chimerax/graphics/opengl.py", line 122 in make_current
chimerax/graphics/opengl.py", line 555 in make_current
chimerax/graphics/opengl.py", line 584 in use_shared_context
chimerax/sideview/tool.py", line 143 in render
chimerax/sideview/tool.py", line 113 in _redraw
chimerax/core/triggerset.py", line 149 in invoke
chimerax/core/triggerset.py", line 248 in _activate
chimerax/core/triggerset.py", line 217 in activate
chimerax/core/triggerset.py", line 393 in activate_trigger
chimerax/core/updateloop.py", line 100 in draw_new_frame
chimerax/core/updateloop.py", line 169 in update_graphics_now
chimerax/ui/graphics.py", line 153 in resizeEvent
chimerax/ui/graphics.py", line 61 in event
chimerax/ui/gui.py", line 368 in event_loop
chimerax/core/__main__.py", line 1057 in init
chimerax/core/__main__.py", line 1220 in

I tried showing side view and a large model and resizing the main window, full lighting, but could not get a crash in ChimeraX 1.10.1 on macOS 15.6.1.

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