![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 hours ago
Closed 2 hours ago
#19735 closed defect (duplicate)
Crash when window moved and/or maximized in QDockWidget::event()
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-26.2-arm64-arm-64bit
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000000316c67000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000317c73000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000030704f000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000306043000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000305037000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 948 in wait
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000030402b000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000030301f000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000302013000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000301007000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017f357000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017e34b000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017d33f000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017c333000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017b327000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017a31b000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017930f000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000178303000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Current thread 0x00000001f95e2c40 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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.surface._surface, chimerax.pdb_lib._load_libs, PIL._imaging, chimerax.map._map, 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, 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 (total: 56)
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{
"uptime" : 95000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "Mac14,13",
"coalitionID" : 12578,
"osVersion" : {
"train" : "macOS 26.2",
"build" : "25C56",
"releaseType" : "User"
},
"captureTime" : "2026-01-16 09:43:13.2695 -0600",
"codeSigningMonitor" : 2,
"incident" : "E1136CF0-E5E7-4569-97CC-8C6527489383",
"pid" : 1210,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-01-16 09:27:59.4747 -0600",
"procStartAbsTime" : 2265823630820,
"procExitAbsTime" : 2287754516312,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.11.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.11.0","CFBundleVersion":"1.11.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"813FDA0D-8D55-5BE8-A95F-7D83FE67D131","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "A1E8D024-5023-B02A-B74F-CB56AAE7B5BC",
"appleIntelligenceStatus" : {"reasons":["notOptedIn","siriAssetIsNotReady","assetIsNotReady"],"state":"unavailable"},
"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" : "3591EC76-7425-4722-99AB-E69EB850F3B2",
"sip" : "enabled",
"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4370726904
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 104840000-104844000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":1210},
"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4370726904
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 104840000-104844000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.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" : [{
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CG image 48K 3
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CoreAnimation 2432K 146
CoreGraphics 96K 6
CoreUI image data 1728K 22
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page table in kernel 1538K 1
shared memory 3664K 23
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===== Log before crash start =====
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/dd32968/Library/CloudStorage/Box-
> Box/Experiments/AlphaFold/Par3_Par6_aPKC/Par3_PAR3_aPKC.cxs
Log from Fri Sep 19 13:31:37 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/dd32968/Library/CloudStorage/Box-
> Box/Experiments/AlphaFold/Par3_PAR3_aPKC.cxs format session
Log from Fri Sep 19 13:05:03 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> set bgColor #04040400
> set bgColor #5d5d5d00
> set bgColor #73737300
> set bgColor #98989800
> set bgColor #b2b2b200
> set bgColor #eaeaea00
> set bgColor #ffffff00
No presets found in custom preset folder
/Users/dd32968/Documents/ChimeraX_presets
> toolshed show
Downloading bundle chimerax_clix-0.2.4-py3-none-any.whl
/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkginfo/distribution.py:175: NewMetadataVersion: New metadata version
(2.4) higher than latest supported version: parsing as 2.3
warnings.warn(NewMetadataVersion(self.metadata_version))
Installed ChimeraX-clix (0.2.4)
> ui tool show CliX
> alphafold fetch G5EEG8 pae true
Fetching compressed AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching url https://alphafold.ebi.ac.uk/files/AF-G5EEG8-F1-model_v3.cif
failed:
HTTP Error 404: Not Found
> alphafold fetch F5GZI3 pae true
Fetching compressed AlphaFold F5GZI3 from
https://alphafold.ebi.ac.uk/files/AF-F5GZI3-F1-model_v3.cif
Chain information for AlphaFold F5GZI3 #1
---
Chain | Description | UniProt
A | Partitioning defective 3 homolog | F5GZI3_HUMAN 1-747
Color AlphaFold F5GZI3 by residue attribute pLDDT_score
Fetching compressed AlphaFold PAE F5GZI3 from
https://alphafold.ebi.ac.uk/files/AF-F5GZI3-F1-predicted_aligned_error_v3.json
> open F5GZI3 fromDatabase uniprot associate #1/A
Summary of feedback from opening F5GZI3 fetched from uniprot
---
notes | Fetching compressed F5GZI3 UniProt info from https://www.uniprot.org/uniprot/F5GZI3.xml
Alignment identifier is F5GZI3
Associated AlphaFold F5GZI3 chain A to F5GZI3 with 0 mismatches
Opened UniProt F5GZI3
> select /A:652-666,681-722
466 atoms, 466 bonds, 57 residues, 1 model selected
> select /A:1-77,191-276,307-382
1811 atoms, 1826 bonds, 239 residues, 1 model selected
> select /A:138-178,578-600,645-747
1278 atoms, 1296 bonds, 167 residues, 1 model selected
> select /A:1-77,191-276,307-382
1811 atoms, 1826 bonds, 239 residues, 1 model selected
> select /A:1-77,191-276,307-382
1811 atoms, 1826 bonds, 239 residues, 1 model selected
> cartoon style protein thickness 3.5 width 3.5
> cartoon style protein thickness 2 width 2
> graphics silhouettes true
> lighting soft
> color red
> color gradient
Missing or invalid "surfaces" argument: empty atom specifier
> select /A:1-77,191-276,307-382
1811 atoms, 1826 bonds, 239 residues, 1 model selected
> select /A:1-77,191-276,307-382
1811 atoms, 1826 bonds, 239 residues, 1 model selected
> color #1 #eda60eff
> color #1 #eaed66ff
> color byattribute domain
No known/registered numeric attribute domain
> ~select
Nothing selected
> select /A:652-666,681-722
466 atoms, 466 bonds, 57 residues, 1 model selected
> select /A:1-77,191-276,307-382
1811 atoms, 1826 bonds, 239 residues, 1 model selected
> select /A:138-178,578-600,645-747
1278 atoms, 1296 bonds, 167 residues, 1 model selected
> select /A:1-77,191-276,307-382
1811 atoms, 1826 bonds, 239 residues, 1 model selected
> select /A:1-77,191-276,307-382
1811 atoms, 1826 bonds, 239 residues, 1 model selected
> ~select
Nothing selected
> select /A:652-666,681-722
466 atoms, 466 bonds, 57 residues, 1 model selected
> select /A:1-77,191-276,307-382
1811 atoms, 1826 bonds, 239 residues, 1 model selected
> select /A:138-178,578-600,645-747
1278 atoms, 1296 bonds, 167 residues, 1 model selected
> select /A:1-77,191-276,307-382
1811 atoms, 1826 bonds, 239 residues, 1 model selected
> hide #1 models
> show #1 models
> select add #1
5760 atoms, 5850 bonds, 747 residues, 1 model selected
> select subtract #1
Nothing selected
> color byattribute r:avg #!1 palette bluered key true
Unknown/unregistered Residue attribute avg
> close all
Desktop color scheme is dark
Desktop color scheme is light
> alphafold interfaces /Users/dd32968/Library/CloudStorage/Box-
> Box/Experiments/AlphaFold/fold_par_3_par_6_apkc
1 of 1 dimers have 10 or more confident residue interactions
spanning open /Users/dd32968/Library/CloudStorage/Box-
> Box/Experiments/AlphaFold/fold_par_3_par_6_apkc/fold_par_3_par_6_apkc_model_4.cif
Chain information for fold_par_3_par_6_apkc_model_4.cif #1
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> rename last-opened par_3_par_6_apkc
> color last-opened bypolymer
> select
> /A:16,18,21,22,23,24,25,26,27,28,29,50,51,52,90,218,220,225,229,232,233,236,237,242,498,499,500,502,503,506,524,525,526,527,528,529,530,531,532,542,544,545,546,547,548,575,579,583,854,856,860,861,862,863,864,865,866/B:59,60,61,63,64,65,66,68,69,71,72,75,78,79,100,101,102,103,263,264,302,306,307,309,310,311,312,338,340,341,343,344,347,366,367,370,371,377,379,380,381,398,411,412,413,414,415,416,417,418,444,448,449,465,534,535,582,584,585,586,588,589,591,592,593,594,595,596,597
> & last-opened
621 atoms, 596 bonds, 81 residues, 1 model selected
> alphafold pae last-opened file /Users/dd32968/Library/CloudStorage/Box-
> Box/Experiments/AlphaFold/fold_par_3_par_6_apkc/fold_par_3_par_6_apkc_full_data_4.json
> alphafold contacts last-opened & /A toAtoms last-opened & /B distance 4
> maxPae 5
Found 8 residue or atom pairs within distance 4 with pae name frozen interface sel
> rainbow chains palette bupu
> color sel blue
> select \A
Expected an objects specifier or a keyword
> select /A
10496 atoms, 10696 bonds, 1379 residues, 1 model selected
> select none
Expected an objects specifier or a keyword
> select
17688 atoms, 18045 bonds, 8 pseudobonds, 2285 residues, 2 models selected
> ~select
Nothing selected
> ~select
Nothing selected
> ~select
Nothing selected
> ~select
Nothing selected
> color /A:60-151 lime
> name frozen P3-OD
Missing or invalid "objects" argument: empty atom specifier
> name frozen P3-OD sel
Nothing is selected by specifier
> color /A:64-157 lime
> color /A:68-155 lime
> name frozen P3-OD /A:68-155
> color /A:375-497 lime
> name frozen P3-PDZ1 /A:395-497
> ui tool show "Color Key"
> ui mousemode right "color key"
> ui tool show "Color Key"
> ui mousemode right "color key"
> key delete
> color /A:495-588 lime
> color /A:501-600 lime
> name frozen P3-PDZ2 /A:501-600
> color /A:655-765 lime
> name frozen P3-PDZ3 /A:656:765
> color P3-PDZ3 lime
> color ~P3-PDZ3 grey
> name frozen P3-PDZ3 /A:656-765
> color P3-PDZ3 lime
> color ~P3-PDZ3 grey
> name frozen P3-PDZ3 /A:650-760
> color ~P3-PDZ3 grey
> name frozen P3-PDZ3 /A:650-755
> color ~P3-PDZ3 grey
> color P3-PDZ3 lime
> name frozen P3-PDZ3 /A:653-755
> color /A:837-907 lime
> name frozen P3-S827 /A:827
> color P3-S827 red
> sequence chain #1/A
Alignment identifier is 1/A
> select
> /A:2-12,14-41,47-57,90-104,133-135,159-171,175-182,185-203,213-219,222-231,248-251,254-276,289-298,300-323,325-327,338-366,392-395,407-409,433-437,454-456,459-471,485-493,501-505,570-572,575-584,606-609,612-626,628-630,632-636,663-665,702-706,728-744,761-771,779-786,795-806,813-820,832-845,852-854,866-868,875-889,905-911,913-922,927-937,940-979,989-1008,1017-1030,1038-1049,1056-1066,1071-1080,1095-1124,1129-1131,1135-1146,1148-1159,1162-1175,1177-1186,1191-1205,1209-1217,1219-1238,1240-1250,1255-1267,1270-1289,1291-1298,1303-1317,1324-1333,1337-1346,1348-1360,1367-1378
5946 atoms, 5991 bonds, 771 residues, 1 model selected
> select /A:854
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:854-871
140 atoms, 140 bonds, 18 residues, 1 model selected
> select /A:854-871
140 atoms, 140 bonds, 18 residues, 1 model selected
> select /A:854
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:854-869
128 atoms, 128 bonds, 16 residues, 1 model selected
> name frozen P3-CR3 sel
> color P3-CR3 red
> select /A:863
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:863
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 6 atom styles
> style sel sphere
Changed 6 atom styles
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
[Repeated 1 time(s)]
> show sel atoms
> color sel byhetero
[Repeated 1 time(s)]
> color /B:15-117 lime
> sequence chain #1/B
Alignment identifier is 1/B
> sequence chain #1/C
Alignment identifier is 1/C
> select /C:170
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /C:23-170
1217 atoms, 1245 bonds, 148 residues, 1 model selected
> color /B:20-114 lime
> color /B:57 lime
> color /B:36 magenta
> color /B:11-130 lime
> name frozen P6-PB1 sel
> select all
17688 atoms, 18045 bonds, 8 pseudobonds, 2285 residues, 2 models selected
> color bychain
> color /B:138-268 lime
> name frozen P6-CPDZ sel
> name frozen P6-CPDZ /B:138-247
> color PD-CPDZ lime
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color P6-CPDZ lime
> color ~P6-CPDZ gray
> name frozen P6-CPDZ /B:155-247
> color ~P6-CPDZ gray
> color /C:10-118 lime
> color /C:12-106 lime
> name frozen KC-PB1 /C:12-95
> color /C:112-191 lime
> name frozen KC-C1 /C:120-191
> color /C:247-597 lime
> name frozen KC-KD /C:247-588
> color
> select /A:1379
13 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:1375-1379
51 atoms, 53 bonds, 5 residues, 1 model selected
> name frozen KC-PBM sel
> rainbow chains palette bupu
> ui tool show "Color Actions"
> color P3-OD Greys3
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color P3-OD greys-5(3)
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel light salmon
> select all
17688 atoms, 18045 bonds, 8 pseudobonds, 2285 residues, 2 models selected
> color sel white
> select P3-OD
691 atoms, 699 bonds, 88 residues, 1 model selected
> color sel light gray
> color sel gray
> color sel dark gray
> color sel dim gray
> rainbow PD-OD P3-PDZ1 P3-PDZ2 P3-PDZ3 P3-CR3 palette OrRd level
Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword
> select P3-*
Expected an objects specifier or a keyword
> select P3* objects
Expected an objects specifier or a keyword
> color byrainbow P3-OD P3-PDZ1 P3-PDZ2
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /A RdPu1
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel OrRd-5-1
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel OrRd-5
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel OrRd
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
FYI: command is replacing existing command: "palette list"
> OrRd-9
Unknown command: palette OrRd-9
> color name purple1 #feebe2
Color 'purple1' is opaque: rgb(99.6%, 92.2%, 88.6%) hex: #feebe2
> color /A purple1
> color sel purple
> color sel lavender
[Repeated 1 time(s)]
> select /A
10496 atoms, 10696 bonds, 1379 residues, 1 model selected
> color sel lavender
> color sel thistle
> color P3-OD Plum
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select P3-OD
691 atoms, 699 bonds, 88 residues, 1 model selected
> color sel plum
> color sel medium purple
> select P3-PDZ1
774 atoms, 780 bonds, 103 residues, 1 model selected
> color sel medium slate blue
> color sel dark slate blue
> color sel slate blue
> color sel medium slate blue
> color sel medium orchid
> color sel dark orchid
> color sel medium slate blue
> color name purple1 #dadaeb
Color 'purple1' is opaque: rgb(85.5%, 85.5%, 92.2%) hex: #dadaeb
> color name purple2 #bcbddc
Color 'purple2' is opaque: rgb(73.7%, 74.1%, 86.3%) hex: #bcbddc
> color name purple3 #9e9ac8
Color 'purple3' is opaque: rgb(62%, 60.4%, 78.4%) hex: #9e9ac8
> color name purple4 #807dba
Color 'purple4' is opaque: rgb(50.2%, 49%, 72.9%) hex: #807dba
> color name purple5 #6a51a3
Color 'purple5' is opaque: rgb(41.6%, 31.8%, 63.9%) hex: #6a51a3
> color name purple6 #4a1486
Color 'purple6' is opaque: rgb(29%, 7.84%, 52.5%) hex: #4a1486
> color name red1 #fee0d2
Color 'red1' is opaque: rgb(99.6%, 87.8%, 82.4%) hex: #fee0d2
> color name red2 #fcbba1
Color 'red2' is opaque: rgb(98.8%, 73.3%, 63.1%) hex: #fcbba1
> color name red3 #fc9272
Color 'red3' is opaque: rgb(98.8%, 57.3%, 44.7%) hex: #fc9272
> color name red4 #fb6a4a
Color 'red4' is opaque: rgb(98.4%, 41.6%, 29%) hex: #fb6a4a
> color name red5 #ef3b2c
Color 'red5' is opaque: rgb(93.7%, 23.1%, 17.3%) hex: #ef3b2c
> color name red6 #cb181d
Color 'red6' is opaque: rgb(79.6%, 9.41%, 11.4%) hex: #cb181d
> color name red7 #99000d
Color 'red7' is opaque: rgb(60%, 0%, 5.1%) hex: #99000d
> color name green1 #e5f5e0
Color 'green1' is opaque: rgb(89.8%, 96.1%, 87.8%) hex: #e5f5e0
> color name green2 #c7e9c0
Color 'green2' is opaque: rgb(78%, 91.4%, 75.3%) hex: #c7e9c0
> color name green3 #a1d99b
Color 'green3' is opaque: rgb(63.1%, 85.1%, 60.8%) hex: #a1d99b
> color name green4 #74c476
Color 'green4' is opaque: rgb(45.5%, 76.9%, 46.3%) hex: #74c476
> color name green5 #41ab5d
Color 'green5' is opaque: rgb(25.5%, 67.1%, 36.5%) hex: #41ab5d
> color name green6 #238b45
Color 'green6' is opaque: rgb(13.7%, 54.5%, 27.1%) hex: #238b45
> color name green7 #005a32
Color 'green7' is opaque: rgb(0%, 35.3%, 19.6%) hex: #005a32
> color name blue1 #deebf7
Color 'blue1' is opaque: rgb(87.1%, 92.2%, 96.9%) hex: #deebf7
> color name blue2 #c6dbef
Color 'blue2' is opaque: rgb(77.6%, 85.9%, 93.7%) hex: #c6dbef
> color name blue3 #9ecae1
Color 'blue3' is opaque: rgb(62%, 79.2%, 88.2%) hex: #9ecae1
> color name blue4 #6baed6
Color 'blue4' is opaque: rgb(42%, 68.2%, 83.9%) hex: #6baed6
> color name blue5 #4292c6
Color 'blue5' is opaque: rgb(25.9%, 57.3%, 77.6%) hex: #4292c6
> color name blue6 #2171b5
Color 'blue6' is opaque: rgb(12.9%, 44.3%, 71%) hex: #2171b5
> color name blue7 #084594
Color 'blue7' is opaque: rgb(3.14%, 27.1%, 58%) hex: #084594
> color /A purple1
> color /A purple2
> color P3-CR3 purple6
> color P3-PDZ3 purple5
> color P3-PDZ2 purple4
> color P3-PDZ1 purple3
> color P3-OD purple2
> color /A purple1
> color P3-OD purple2
> color P3-PDZ1 purple3
> color P3-PDZ2 purple4
> color P3-PDZ3 purple5
> color P3-CR3 purple6
> color P3-OD purple6
> color /A:342 lime
> color /A:351 magenta
> color /A purple1
> color P3-OD purple2
> color P3-PDZ1 purple3
> color P3-PDZ2 purple4
> color P3-PDZ3 purple5
> color P3-CR3 purple6
> color P3-OD purple6
> name frozen P3-PDZ1 /A:385-497
> color P3-PDZ1 purple3
> name frozen P3-PDZ1 /A:371-497
> color P3-PDZ1 purple3
> name frozen P3-PDZ1 /A:371-481
> color P3-PDZ1 purple3
> color /A:482-497 purple1
> color /B red1
> color /B red2
> color P6-PB1 red4
> select KC-PB1
674 atoms, 685 bonds, 84 residues, 1 model selected
> color P6-CPDZ red6
> select P6-PB1
1217 atoms, 1245 bonds, 148 residues, 1 model selected
> select P6-CPDZ
709 atoms, 715 bonds, 93 residues, 1 model selected
> name frozen P6-PB1 /B:13-95
> color P6-PB1 red4
> color /C blue2
> color /C blue3
> color KC-PB1 blue4
> color KC-C1 blue5
> color KC-KD blue7
> color KC-KD blue6
> color KC-PBM blue7
> color KC-PBM purple2
> select /C:597
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:593-597
42 atoms, 41 bonds, 5 residues, 1 model selected
> name frozen KC-PBM sel
> color KC-PBM blue7
> name frozen P3-iPBM /A:235-240
> color P3-iPBM purple4
> color P3-iPBM purple5
> color P3-iPBM purple6
> select P3-iPBM
46 atoms, 46 bonds, 6 residues, 1 model selected
> color purple2
> undo color
Expected fewer arguments
> undo
> color sel purple2
> name frozen P3-iPBM /A:232-238
> color P3-iPBM purple6
> select
> /B:14-21,24-31,58-63,69-71,88-95,155-160,170-180,185-196,213-217,241-246
614 atoms, 615 bonds, 73 residues, 1 model selected
> select /B:69-70
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /B:69-125
469 atoms, 478 bonds, 57 residues, 1 model selected
> select /B:66
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:1-66
539 atoms, 555 bonds, 66 residues, 1 model selected
> save /Users/dd32968/Library/CloudStorage/Box-
> Box/Experiments/AlphaFold/Par3_PAR3_aPKC.cxs
——— End of log from Fri Sep 19 13:05:03 2025 ———
> view name session-start
opened ChimeraX session
> ui tool show CliX
> select ::bfactor>40
Nothing selected
> select @@bfactor>40
9433 atoms, 9574 bonds, 8 pseudobonds, 1238 residues, 2 models selected
> select @@bfactor hide sel cartoons
> show sel cartoons
> select @@bfactor select @@bfactor hide sel cartoons
> select @@bfactor hide sel cartoons
> select @@bfactor select @@plddt select ::plddt ~select
Nothing selected
> ~select ::plddt ~select ::bfactor ~select @@bfactor select @@bfactor hide sel cartoons
> select KC-C1
598 atoms, 614 bonds, 72 residues, 1 model selected
> show sel cartoons
> select KC-KD
2780 atoms, 2848 bonds, 342 residues, 1 model selected
> show sel cartoons
> show KC-PB1
> show KC-PB1 cartoons
> hide KC-PB1 stick
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide KC-PB1
> show P6-PB1 cartoons
> show P6-CPDZ cartoons
> show P3-OD cartoons
> show P3-PB1 cartoons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show P3-PDZ1 cartoons
> show P3-PDZ2 cartoons
> show P3-PDZ3 cartoons
> show P3-CR3 cartoons
> show P3-PBM cartoons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show P3-iPBM cartoons
> select KC-PBM
42 atoms, 41 bonds, 5 residues, 1 model selected
> show sel cartoons
> save /Users/dd32968/Library/CloudStorage/Box-
> Box/Experiments/AlphaFold/Par3_PAR3_aPKC.cxs
——— End of log from Fri Sep 19 13:31:37 2025 ———
> view name session-start
opened ChimeraX session
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file /Users/dd32968/Library/CloudStorage/Box-
> Box/Experiments/AlphaFold/Par3_Par6_aPKC/fold_par_3_par_6_apkc/fold_par_3_par_6_apkc_summary_confidences_0.json
JSON file "/Users/dd32968/Library/CloudStorage/Box-
Box/Experiments/AlphaFold/Par3_Par6_aPKC/fold_par_3_par_6_apkc/fold_par_3_par_6_apkc_summary_confidences_0.json"
is not AlphaFold predicted aligned error data, expected a top level list
> open /Users/dd32968/Library/CloudStorage/Box-
> Box/Experiments/AlphaFold/Par3_Par6_aPKC/fold_par_3_par_6_apkc/fold_par_3_par_6_apkc_summary_confidences_0.json
Failed opening file /Users/dd32968/Library/CloudStorage/Box-
Box/Experiments/AlphaFold/Par3_Par6_aPKC/fold_par_3_par_6_apkc/fold_par_3_par_6_apkc_summary_confidences_0.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/dd32968/Library/CloudStorage/Box-
Box/Experiments/AlphaFold/Par3_Par6_aPKC/fold_par_3_par_6_apkc/fold_par_3_par_6_apkc_summary_confidences_0.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
> open /Users/dd32968/Library/CloudStorage/Box-
> Box/Experiments/AlphaFold/Par3_Par6_aPKC/fold_par_3_par_6_apkc/fold_par_3_par_6_apkc_summary_confidences_0.json
Failed opening file /Users/dd32968/Library/CloudStorage/Box-
Box/Experiments/AlphaFold/Par3_Par6_aPKC/fold_par_3_par_6_apkc/fold_par_3_par_6_apkc_summary_confidences_0.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/dd32968/Library/CloudStorage/Box-
Box/Experiments/AlphaFold/Par3_Par6_aPKC/fold_par_3_par_6_apkc/fold_par_3_par_6_apkc_summary_confidences_0.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
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file /Users/dd32968/Library/CloudStorage/Box-
> Box/Experiments/AlphaFold/Par3_Par6_aPKC/fold_par_3_par_6_apkc/fold_par_3_par_6_apkc_full_data_0.json
> select
> /A:2-12,14-41,47-57,90-104,133-135,159-171,175-182,185-203,213-219,222-231,248-251,254-276,289-298,300-323,325-327,338-366,392-395,407-409,433-437,454-456,459-471,485-493,501-505,570-572,575-584,606-609,612-626,628-630,632-636,663-665,702-706,728-744,761-771,779-786,795-806,813-820,832-845,852-854,866-868,875-889,905-911,913-922,927-937,940-979,989-1008,1017-1030,1038-1049,1056-1066,1071-1080,1095-1124,1129-1131,1135-1146,1148-1159,1162-1175,1177-1186,1191-1205,1209-1217,1219-1238,1240-1250,1255-1267,1270-1289,1291-1298,1303-1317,1324-1333,1337-1346,1348-1360,1367-1378
5946 atoms, 5991 bonds, 771 residues, 1 model selected
> select
> /A:69-74,77-82,115-120,144-148,235-237,371-373,380-384,399-404,422-428,446-449,477-481,512-519,527-533,539-543,561-565,590-597,655-661,673-681,687-689,691-697,714-718,748-754,1085-1088
1052 atoms, 1042 bonds, 131 residues, 1 model selected
> select /A:240
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:230-240
89 atoms, 89 bonds, 11 residues, 1 model selected
> select /A:238
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:231-238
61 atoms, 60 bonds, 8 residues, 1 model selected
> color /A:209 lime
> color /A:218 magenta
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11 (2025-12-17)
© 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 M2 Max
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac14,13
Model Number: Z17Z0006VLL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 64 GB
System Firmware Version: 13822.61.10
OS Loader Version: 13822.61.10
Software:
System Software Overview:
System Version: macOS 26.2 (25C56)
Kernel Version: Darwin 25.2.0
Time since boot: 1 day, 2 hours, 29 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
DELL U2724D:
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
ARZOPA:
Resolution: 900 x 1600
UI Looks like: 900 x 1600 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: 270
ARZOPA:
Resolution: 900 x 1600
UI Looks like: 900 x 1600 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: 90
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
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: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.0.0
roman-numerals-py: 4.0.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.0.4
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
Change History (2)
comment:1 by , 5 hours ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash when window moved and/or maximized |
comment:2 by , 2 hours ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash when window moved and/or maximized → Crash when window moved and/or maximized in QDockWidget::event() |
Since December we have seen a dozen reports of this crash in QDockWidget::event(). Also there are 164 bug reports containing QDockWidget::event() but with different stack traces going back years. Our best hope is that Qt 6.10 fixes this Qt bug.
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Looks awfully similar to #19712