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Opened 8 days ago
Closed 8 days ago
#19702 closed defect (duplicate)
Crash on Mac waking from sleep
| 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-13.5.2-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Thread 0x00000002ade7b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002ace6f000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002abe63000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002aae57000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a9e4b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a8e3f000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a7e33000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a6e27000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a5e1b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a4e0f000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000297693000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000296687000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029567b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029466f000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000293663000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001f490e080 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imaging, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 50)
{"app_name":"ChimeraX","timestamp":"2026-01-08 12:56:11.00 -0500","app_version":"1.10.0","slice_uuid":"9cf8124a-d876-34ad-b7ee-c011183ebc15","build_version":"1.10.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.5.2 (22G91)","roots_installed":0,"name":"ChimeraX","incident_id":"52EE29FA-25BE-4F83-BDBE-5F91576168DC"}
{
"uptime" : 1500000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,6",
"coalitionID" : 7869,
"osVersion" : {
"train" : "macOS 13.5.2",
"build" : "22G91",
"releaseType" : "User"
},
"captureTime" : "2026-01-08 12:56:09.4054 -0500",
"incident" : "52EE29FA-25BE-4F83-BDBE-5F91576168DC",
"pid" : 78030,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-12-17 09:38:45.5504 -0500",
"procStartAbsTime" : 32981471257570,
"procExitAbsTime" : 37015694014359,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"5941FB0E-C42A-5606-8409-DA443B737AF0","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "7F0B2FC0-5520-8CAC-651A-4D90B0F6E43F",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"sleepWakeUUID" : "6F092198-B16C-4C72-90A3-260E12147496",
"sip" : "enabled",
"vmRegionInfo" : "0x5d50941d670 is not in any region. Bytes after previous region: 5931505145457 Bytes before following region: 99140574783888\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x000005d50941d670","rawCodes":[1,6412541482608],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000005d50941d670"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":78030},
"vmregioninfo" : "0x5d50941d670 is not in any region. Bytes after previous region: 5931505145457 Bytes before following region: 99140574783888\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] 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" : [{"triggered":true,"id":17381136,"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":5100698264},{"value":80},{"value":109},{"value":6160170400},{"value":4550402337},{"value":956487967706333814},{"value":956487966438630134},{"value":14757395258967641293},{"value":4294967286},{"value":5100698194},{"value":0},{"value":53},{"value":4294967280},{"value":328},{"value":8476898208},{"value":0},{"value":11},{"value":8398102656,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8398102880,"symbolLocation":224,"symbol":"_main_thread"},{"value":1},{"value":4325557808,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8355758080,"symbolLocation":0,"symbol":"OBJC_IVAR_$__NSSliderCellDataDrivenMetrics._state"},{"value":8355758080,"symbolLocation":0,"symbol":"OBJC_IVAR_$__NSSliderCellDataDrivenMetrics._state"},{"value":5},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6870842408},"cpsr":{"value":1073745920},"fp":{"value":5100698336},"sp":{"value":5100698304},"esr":{"value":1442840704,"description":" 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===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/om/Downloads/ODC_M1/ODC_M1 protein-refined_017.pdb"
Chain information for ODC_M1 protein-refined_017.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
G | No description available
H | No description available
I | No description available
> show cartoons
> hide atoms
> select /B:268-574
2500 atoms, 2554 bonds, 307 residues, 1 model selected
> select /B:268-574
2500 atoms, 2554 bonds, 307 residues, 1 model selected
> select add #1
21270 atoms, 21800 bonds, 13 pseudobonds, 2551 residues, 2 models selected
> select subtract #1
Nothing selected
> select /B:367
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
> open "/Users/om/Downloads/FINAL ODC_M1 protein-refined_017.pdb"
Chain information for FINAL ODC_M1 protein-refined_017.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
G | No description available
H | No description available
I | No description available
> open /Users/om/Downloads/D_9100124238_val-data_P1.cif
Summary of feedback from opening /Users/om/Downloads/D_9100124238_val-
data_P1.cif
---
warning | No mmCIF models found.
> open /Users/om/Downloads/D_9100124238_val-data_P1.cif
Summary of feedback from opening /Users/om/Downloads/D_9100124238_val-
data_P1.cif
---
warning | No mmCIF models found.
Desktop color scheme is dark
Desktop color scheme is light
> open /Volumes/current/fsc_example.xml
Opened fsc_example.xml
> open /Users/om/Downloads/Final_PDB/J177_fsc.xml
Opened J177_fsc.xml
> show sel cartoons
> hide sel atoms
> select add #1
21270 atoms, 21800 bonds, 13 pseudobonds, 2551 residues, 2 models selected
> select add #2
42540 atoms, 43600 bonds, 26 pseudobonds, 5102 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> hide #!2 models
> select subtract #2
21270 atoms, 21800 bonds, 13 pseudobonds, 2551 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/H #2/H
Alignment identifier is 1
> select #1/H:1 #2/H:1
44 atoms, 48 bonds, 2 residues, 2 models selected
> select #1/H #2/H
1192 atoms, 1332 bonds, 58 residues, 2 models selected
1 [ID: 1] region 2 chains [1-29] RMSD: 0.000
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
> open "/Users/om/Downloads/Final_PDB/FINAL HsODC_protein.pdb"
Chain information for FINAL HsODC_protein.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
G | No description available
H | No description available
I | No description available
> select add #2
21866 atoms, 22466 bonds, 13 pseudobonds, 2580 residues, 3 models selected
> select subtract #2
596 atoms, 666 bonds, 29 residues, 1 model selected
> select add #1
21270 atoms, 21800 bonds, 13 pseudobonds, 2551 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 atoms
> show #!3 cartoons
> select #3/A:468-860
3063 atoms, 3115 bonds, 1 pseudobond, 388 residues, 2 models selected
> ui tool show "Color Actions"
> color sel bychain
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:468-860
3063 atoms, 3115 bonds, 1 pseudobond, 388 residues, 2 models selected
> split #3
Split FINAL HsODC_protein.pdb (#3) into 8 models
Chain information for FINAL HsODC_protein.pdb A #3.1
---
Chain | Description
A | No description available
Chain information for FINAL HsODC_protein.pdb B #3.2
---
Chain | Description
B | No description available
Chain information for FINAL HsODC_protein.pdb C #3.3
---
Chain | Description
C | No description available
Chain information for FINAL HsODC_protein.pdb D #3.4
---
Chain | Description
D | No description available
Chain information for FINAL HsODC_protein.pdb E #3.5
---
Chain | Description
E | No description available
Chain information for FINAL HsODC_protein.pdb G #3.6
---
Chain | Description
G | No description available
Chain information for FINAL HsODC_protein.pdb H #3.7
---
Chain | Description
H | No description available
Chain information for FINAL HsODC_protein.pdb I #3.8
---
Chain | Description
I | No description available
> color #3.1 darkseagreen
> color #3.2 burlywood
> color #3.3 coral
> color #3.4 #498cffff
> color #3.5 mediumslateblue
> color #3.6 hotpink
> color #3.7 lightseagreen
> color #3.8 #ebebebff
> color #3.8 #d6d6d6ff
> color #3.8 #00fdffff
> color #3.8 #fffb00ff
> color #3.8 #8efa00ff
> color #3.8 #73fcd6ff
> color #3.8 #73fdffff
> color #3.8 #76d6ffff
> color #3.8 #73fcd6ff
> sequence chain #3.2/B
Alignment identifier is 3.2/B
> select #3.2/B:363
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.2/B:363-369
55 atoms, 55 bonds, 7 residues, 1 model selected
> select add #3.2
2500 atoms, 2554 bonds, 307 residues, 1 model selected
> select subtract #3.2
Nothing selected
> select add #3.2
2500 atoms, 2554 bonds, 307 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #3.2/B:369
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.2/B:363-369
55 atoms, 55 bonds, 7 residues, 1 model selected
> show sel cartoons
> select add #3.2
2500 atoms, 2554 bonds, 307 residues, 1 model selected
> select subtract #3.2
Nothing selected
> sequence chain #3.3/C
Alignment identifier is 3.3/C
> select #3.3/C:177
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.3/C:177
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #3.3/C:178
17 atoms, 16 bonds, 2 residues, 1 model selected
> select add #3.3/C:179
29 atoms, 28 bonds, 3 residues, 1 model selected
> select add #3.3/C:180
35 atoms, 33 bonds, 4 residues, 1 model selected
> select add #3.3
4897 atoms, 5000 bonds, 6 pseudobonds, 606 residues, 2 models selected
> hide sel cartoons
> select #3.3/C:177
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.3/C:177-181
43 atoms, 44 bonds, 5 residues, 1 model selected
> show sel cartoons
> select #3.3/C:181
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.3/C:181
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select add #3.3
4897 atoms, 5000 bonds, 6 pseudobonds, 606 residues, 2 models selected
> select subtract #3.3
Nothing selected
> select add #3.3
4897 atoms, 5000 bonds, 6 pseudobonds, 606 residues, 2 models selected
> show sel cartoons
> select subtract #3.3
Nothing selected
> select #3.3/C:698
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.3/C:693-698
41 atoms, 41 bonds, 6 residues, 1 model selected
> select #3.3/C:693
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.3/C:693-695
24 atoms, 24 bonds, 3 residues, 1 model selected
> select #3.3/C:695
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.3/C:695-700
40 atoms, 40 bonds, 6 residues, 1 model selected
> select add #3.3
4897 atoms, 5000 bonds, 6 pseudobonds, 606 residues, 2 models selected
> select subtract #3.3
Nothing selected
> select add #3.2
2500 atoms, 2554 bonds, 307 residues, 1 model selected
> show sel cartoons
> select subtract #3.2
Nothing selected
> select add #3.4
3438 atoms, 3504 bonds, 422 residues, 1 model selected
> select subtract #3.4
Nothing selected
> select add #3.5
3208 atoms, 3285 bonds, 3 pseudobonds, 393 residues, 2 models selected
> select subtract #3.5
Nothing selected
> select add #3.6
2943 atoms, 2977 bonds, 3 pseudobonds, 375 residues, 2 models selected
> sequence chain #3.6/G
Alignment identifier is 3.6/G
> select #3.6/G:293
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3.6/G:293-298
48 atoms, 48 bonds, 6 residues, 1 model selected
> select #3.6/G:290
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.6/G:290-296
51 atoms, 50 bonds, 7 residues, 1 model selected
> select add #3.6
2943 atoms, 2977 bonds, 3 pseudobonds, 375 residues, 2 models selected
> select subtract #3.6
Nothing selected
> select add #3.1
3095 atoms, 3148 bonds, 1 pseudobond, 390 residues, 2 models selected
> sequence chain #3.1/A
Alignment identifier is 3.1/A
> select #3.1/A:589
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3.1/A:589-597
62 atoms, 62 bonds, 9 residues, 1 model selected
> select add #3.1
3095 atoms, 3148 bonds, 1 pseudobond, 390 residues, 2 models selected
> select subtract #3.1
Nothing selected
> select add #3.1
3095 atoms, 3148 bonds, 1 pseudobond, 390 residues, 2 models selected
> select subtract #3.1
Nothing selected
> select add #3.2
2500 atoms, 2554 bonds, 307 residues, 1 model selected
> select #3.1/A:504
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/A:504-512
79 atoms, 80 bonds, 9 residues, 1 model selected
> select add #3.1
3095 atoms, 3148 bonds, 1 pseudobond, 390 residues, 2 models selected
> select subtract #3.1
Nothing selected
> sequence chain #3.2/B
Alignment identifier is 3.2/B
> select #3.2/B:503
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.2/B:503-511
67 atoms, 68 bonds, 9 residues, 1 model selected
> select #3.2/B:471
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3.2/B:471-574
836 atoms, 851 bonds, 104 residues, 1 model selected
> select #3.2/B:470-471
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #3.2/B:268-471
1670 atoms, 1708 bonds, 204 residues, 1 model selected
> hide sel cartoons
> sequence chain #3.1/A
Alignment identifier is 3.1/A
> select
> #3.1/A:487-494,508-524,540-556,576-588,594-606,622-624,631-641,658-662,665-671,683-693,702-715,719-735,748-758,763-769,772-788,795-809,816-828,837-842,851-859
1743 atoms, 1750 bonds, 214 residues, 1 model selected
> select #3.1/A:769
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/A:468-769
2342 atoms, 2383 bonds, 1 pseudobond, 297 residues, 2 models selected
> select #3.1/A:765
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.1/A:468-765
2312 atoms, 2353 bonds, 1 pseudobond, 293 residues, 2 models selected
> select #3.1/A:763-764
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #3.1/A:468-764
2305 atoms, 2346 bonds, 1 pseudobond, 292 residues, 2 models selected
> select #3.1/A:759
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3.1/A:468-759
2267 atoms, 2307 bonds, 1 pseudobond, 287 residues, 2 models selected
> hide sel cartoons
> sequence chain #2/C
Alignment identifier is 2/C
> select #2/C:707
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:451-707
1640 atoms, 1673 bonds, 2 pseudobonds, 205 residues, 2 models selected
> sequence chain #3.3/C
Alignment identifier is 3.3/C
> select #3.3/C:707
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.3/C:599-707
798 atoms, 813 bonds, 1 pseudobond, 102 residues, 2 models selected
> select
> #3.3/C:26-28,40-64,67-86,111-113,115-126,138-140,144-157,181-192,222-224,227-240,256-260,265-270,281-294,304-316,321-338,340-345,348-356,360-368,370-378,381-387,391-425,435-444,447-449,451-462,465-481,488-500,548-566,570-572,576-578,584-591,595-604,606-608,613-615,628-638,645-660,670-690
3238 atoms, 3267 bonds, 392 residues, 1 model selected
> select #3.3/C:595
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.3/C:595-707
829 atoms, 845 bonds, 1 pseudobond, 106 residues, 2 models selected
> select #3.3/C:594
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.3/C:1-594
4068 atoms, 4154 bonds, 5 pseudobonds, 500 residues, 2 models selected
> hide sel cartoons
> sequence chain #3.4/D
Alignment identifier is 3.4/D
> select #3.4/D:312
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/D:312-431
987 atoms, 1008 bonds, 120 residues, 1 model selected
> select #3.4/D:311
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/D:12-311
2419 atoms, 2462 bonds, 300 residues, 1 model selected
> hide sel cartoons
> select #3.4/D:307
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.4/D:307-311
37 atoms, 36 bonds, 5 residues, 1 model selected
> show sel cartoons
> select #3.4/D:307
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.4/D:307
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select
> #3.4/D:13-30,41-57,73-85,107-118,132-145,161-166,171-181,198-200,204-209,223-234,243-258,260-272,276-289,299-308,313-320,323-338,346-359,369-381,408-416,423-430
1953 atoms, 1968 bonds, 233 residues, 1 model selected
> select #3.4/D:308
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/D:308
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> sequence chain #3.5/E
Alignment identifier is 3.5/E
> select
> #3.5/E:12-22,43-54,69-83,99-111,127-132,137-148,162-164,184-191,201-215,222-236,238-242,250-267,304-318,321-327,349-352,359-369,378-389,413-422,427-430
1632 atoms, 1648 bonds, 196 residues, 1 model selected
> select #3.5/E:321
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.5/E:321-435
790 atoms, 806 bonds, 1 pseudobond, 99 residues, 2 models selected
> select
> #3.5/E:12-22,43-54,69-83,99-111,127-132,137-148,162-164,184-191,201-215,222-236,238-242,250-267,304-318,321-327,349-352,359-369,378-389,413-422,427-430
1632 atoms, 1648 bonds, 196 residues, 1 model selected
> select #3.5/E:314
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3.5/E:314-435
848 atoms, 867 bonds, 1 pseudobond, 106 residues, 2 models selected
> select #3.5/E:303
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.5/E:303-435
939 atoms, 962 bonds, 1 pseudobond, 117 residues, 2 models selected
> select #3.5/E:298
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.5/E:298-435
980 atoms, 1004 bonds, 1 pseudobond, 122 residues, 2 models selected
> select #3.5/E:297-298
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3.5/E:297-435
985 atoms, 1009 bonds, 1 pseudobond, 123 residues, 2 models selected
> select #3.5/E:277
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.5/E:4-277
2191 atoms, 2243 bonds, 1 pseudobond, 268 residues, 2 models selected
> hide sel cartoons
> sequence chain #3.6/G
Alignment identifier is 3.6/G
> select #3.6/G:455
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.6/G:455-557
811 atoms, 817 bonds, 103 residues, 1 model selected
> select #3.6/G:443
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3.6/G:153-443
2092 atoms, 2119 bonds, 2 pseudobonds, 269 residues, 2 models selected
> hide sel cartoons
> ui tool show "Side View"
> lighting simple
> lighting soft
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
No map chosen to save
Permission denied reading directory "/Users/om/Desktop" while trying to
determine next unused file name image#.png.
> cd "/Users/om/Downloads/HsODC WH domain"
Current working directory is: /Users/om/Downloads/HsODC WH domain
> save "/Users/om/Downloads/HsODC WH domain/HsODC WH domains.png" width 1313
> height 830 supersample 4 transparentBackground true
> graphics silhouettes false
> select add #3
21270 atoms, 21800 bonds, 13 pseudobonds, 2551 residues, 13 models selected
> select subtract #3
Nothing selected
> select add #3
21270 atoms, 21800 bonds, 13 pseudobonds, 2551 residues, 13 models selected
> select subtract #3
Nothing selected
> hide #!3 models
> show #!3 models
> select add #3
21270 atoms, 21800 bonds, 13 pseudobonds, 2551 residues, 13 models selected
> show sel cartoons
> select subtract #3
Nothing selected
> select add #3.1
3095 atoms, 3148 bonds, 1 pseudobond, 390 residues, 2 models selected
> select add #3.7
3691 atoms, 3814 bonds, 1 pseudobond, 419 residues, 3 models selected
> select add #3.8
4284 atoms, 4480 bonds, 1 pseudobond, 448 residues, 4 models selected
> nucleotides sel stubs
> style sel stick
Changed 4284 atom styles
> style sel stick
Changed 4284 atom styles
> select subtract #3.1
1189 atoms, 1332 bonds, 58 residues, 2 models selected
> select add #3
21270 atoms, 21800 bonds, 13 pseudobonds, 2551 residues, 13 models selected
> select subtract #3
Nothing selected
> select add #3.7
596 atoms, 666 bonds, 29 residues, 1 model selected
> select add #3.8
1189 atoms, 1332 bonds, 58 residues, 2 models selected
> style sel stick
Changed 1189 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1189 atom styles
> color sel bynucleotide
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1189 atom styles
> style sel stick
Changed 1189 atom styles
> show sel atoms
> nucleotides sel stubs
> color sel bynucleotide
> color #3.7 #73fcd6ff
> color #3.8 #009051ff
> select subtract #3.7
593 atoms, 666 bonds, 29 residues, 1 model selected
> select subtract #3.8
Nothing selected
> sequence chain #3.1/A
Alignment identifier is 3.1/A
> sequence chain #3.1/A
Destroying pre-existing alignment with identifier 3.1/A
Alignment identifier is 3.1/A
> select add #3.1
3095 atoms, 3148 bonds, 1 pseudobond, 390 residues, 2 models selected
> select #3.1/A:597
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.1/A:589-597
62 atoms, 62 bonds, 9 residues, 1 model selected
> select add #3.1
3095 atoms, 3148 bonds, 1 pseudobond, 390 residues, 2 models selected
> hide sel cartoons
> select #3.1/A:589
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3.1/A:589-597
62 atoms, 62 bonds, 9 residues, 1 model selected
> show sel cartoons
> sequence chain #3.2/B
Alignment identifier is 3.2/B
> select add #3.1
3095 atoms, 3148 bonds, 1 pseudobond, 390 residues, 2 models selected
> select subtract #3.1
Nothing selected
> select add #3.2
2500 atoms, 2554 bonds, 307 residues, 1 model selected
> hide sel cartoons
> select #3.2/B:363
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.2/B:363-369
55 atoms, 55 bonds, 7 residues, 1 model selected
> show sel cartoons
> select add #3.2
2500 atoms, 2554 bonds, 307 residues, 1 model selected
> select subtract #3.2
Nothing selected
> sequence chain #3.3/C
Alignment identifier is 3.3/C
> select add #3.3
4897 atoms, 5000 bonds, 6 pseudobonds, 606 residues, 2 models selected
> select subtract #3.3
Nothing selected
> select #3.3/C:158
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3.3/C:158-180
41 atoms, 41 bonds, 1 pseudobond, 5 residues, 2 models selected
> select #3.3/C:177
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.3/C:177-180
35 atoms, 36 bonds, 4 residues, 1 model selected
> select add #3.3
4897 atoms, 5000 bonds, 6 pseudobonds, 606 residues, 2 models selected
> hide sel cartoons
> select #3.3/C:177
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.3/C:177-180
35 atoms, 36 bonds, 4 residues, 1 model selected
> show sel cartoons
> select add #3.3
4897 atoms, 5000 bonds, 6 pseudobonds, 606 residues, 2 models selected
> select subtract #3.3
Nothing selected
> sequence chain #3.4/D
Alignment identifier is 3.4/D
> select #3.4/D:132
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3.4/D:123-132
74 atoms, 75 bonds, 10 residues, 1 model selected
> select #3.4/D:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.4/D:121-132
91 atoms, 92 bonds, 12 residues, 1 model selected
> select #3.4/D:131
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3.4/D:121-131
80 atoms, 80 bonds, 11 residues, 1 model selected
> select add #3.4
3438 atoms, 3504 bonds, 422 residues, 1 model selected
> select subtract #3.4
Nothing selected
> select add #3.4
3438 atoms, 3504 bonds, 422 residues, 1 model selected
> hide sel cartoons
> select #3.4/D:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.4/D:121-131
80 atoms, 80 bonds, 11 residues, 1 model selected
> show sel cartoons
> select add #3.4
3438 atoms, 3504 bonds, 422 residues, 1 model selected
> select subtract #3.4
Nothing selected
> sequence chain #3.6/G
Alignment identifier is 3.6/G
> select #3.6/G:290
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.6/G:290-296
51 atoms, 50 bonds, 7 residues, 1 model selected
> select #3.6/G:294
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.6/G:290-294
36 atoms, 35 bonds, 5 residues, 1 model selected
> select add #3.6
2943 atoms, 2977 bonds, 3 pseudobonds, 375 residues, 2 models selected
> select subtract #3.6
Nothing selected
> select add #3.6
2943 atoms, 2977 bonds, 3 pseudobonds, 375 residues, 2 models selected
> hide sel cartoons
> select #3.6/G:290
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.6/G:290-294
36 atoms, 35 bonds, 5 residues, 1 model selected
> show sel cartoons
> select add #3.6
2943 atoms, 2977 bonds, 3 pseudobonds, 375 residues, 2 models selected
> select subtract #3.6
Nothing selected
> select add #3.5
3208 atoms, 3285 bonds, 3 pseudobonds, 393 residues, 2 models selected
> hide sel cartoons
> ui tool show "Side View"
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes true
> select add #3.3
8105 atoms, 8285 bonds, 9 pseudobonds, 999 residues, 4 models selected
> sequence chain #3.3/C
Alignment identifier is 3.3/C
> select #3.3/C:158
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3.3/C:158-180
41 atoms, 41 bonds, 1 pseudobond, 5 residues, 2 models selected
> show sel cartoons
> select add #3.3
4897 atoms, 5000 bonds, 6 pseudobonds, 606 residues, 2 models selected
> select subtract #3.3
Nothing selected
> save "/Users/om/Downloads/HsODC WH domain/HsODC ISM.png" width 1313 height
> 830 supersample 3
===== Log before crash end =====
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: 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: MacBook Pro
Model Identifier: Mac14,6
Model Number: Z1790005QLL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 8422.141.2
OS Loader Version: 8422.141.2
Software:
System Software Overview:
System Version: macOS 13.5.2 (22G91)
Kernel Version: Darwin 22.6.0
Time since boot: 125 days, 21 hours, 52 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 38
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP E232:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 8 days ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 8 days ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
The ChimeraX bug report panel said what we know about this crash:
"This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX."
ChimeraX 1.11 was released last month with a newer Qt version which we believe has fixed these Mac multi-display crashes.
Note:
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Reported by Om Prakash