![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 16 months ago
Closed 16 months ago
#15574 closed defect (duplicate)
Crash waking Mac up from sleep in displayConfigFinalizedProc, ATI graphics
| 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-13.6.7-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000700024ed7000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700023ed4000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700022ed1000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700021ece000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700020ecb000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001fec8000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001eec5000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001dec2000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001cebf000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001bebc000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001aeb9000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff84a98c7c0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.mlp._mlp, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 60)
{"app_name":"ChimeraX","timestamp":"2024-07-08 19:23:38.00 +0200","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.6.7 (22G720)","roots_installed":0,"name":"ChimeraX","incident_id":"B7A3A45C-213D-44AC-A782-471E87D3E064"}
{
"uptime" : 770000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro14,3",
"coalitionID" : 65269,
"osVersion" : {
"train" : "macOS 13.6.7",
"build" : "22G720",
"releaseType" : "User"
},
"captureTime" : "2024-07-08 19:23:00.3330 +0200",
"incident" : "B7A3A45C-213D-44AC-A782-471E87D3E064",
"pid" : 16048,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-07-08 14:19:58.0488 +0200",
"procStartAbsTime" : 768443511888549,
"procExitAbsTime" : 777933379130879,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"B5FE3AD5-2D67-5EEB-8CB8-5548D4CFE8CF","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "45C7A1E1-B0E4-59CF-FACF-6EA7E4548EF2",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 8,
"bridgeVersion" : {"build":"14Y910","train":"3.0"},
"sleepWakeUUID" : "C0144D35-C006-4189-88ED-56A6B56186CA",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4447883264\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1091d5000-1091d9000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":16048},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4447883264\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1091d5000-1091d9000 [ 16K] r-x\/r-x SM=COW ...acOS\/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" : [{"queue":"com.apple.main-thread","instructionState":{"instructionStream":{"bytes":[41,7,197,252,41,71,32,72,131,199,64,72,131,234,64,119,237,197,252,17,4,23,197,252,17,68,23,32,197,248,119,93,195,72,137,52,23,72,131,234,8,115,246,72,131,194,8,116,11,64,136,116,23,255,72,131,234,1,117,245,93,195,144,144,144,144,144,144,144,144,144,144,144,144,144,144,144,144,85,72,137,229,72,137,249,72,137,250,72,131,231,240,102,15,239,192,102,15,116,7,102,15,215,240,72,131,225,15,72,131,200,255,72,211,224,33,198,116,23,15,188,198,72,41,215,72,1,248,93,195,102,46,15,31,132,0,0,0,0,0,102,144,72,131,199,16,102,15,239,192,102,15,116,7,102,15,215,240,133,246,116,236,235,211,101,72,139,12,37,24,0,0,0,65,137,200,49,192,240,76,15,177,7,15,133,122,31,0,0,233,0,0],"offset":96}},"frames":[{"imageOffset":33174,"symbol":"__pthread_kill","symbolLocation":10,"imageIndex":158},{"imageOffset":24294,"symbol":"pthread_kill","symbolLocation":263,"imageIndex":159},{"imageOffset":271873,"symbol":"raise","symbolLocation":26,"imageIndex":160},{"imageOffset":2540852,"symbol":"faulthandler_fatal_error","symbolLocation":388,"imageIndex":1},{"imageOffset":13805,"symbol":"_sigtramp","symbolLocation":29,"imageIndex":161},{"imageOffset":0,"imageIndex":162},{"imageOffset":38708055,"imageIndex":57},{"imageOffset":38399649,"imageIndex":57},{"imageOffset":36937448,"imageIndex":57},{"imageOffset":36958840,"imageIndex":57},{"imageOffset":108068521,"imageIndex":57},{"imageOffset":108093982,"imageIndex":57},{"imageOffset":82367923,"imageIndex":57},{"imageOffset":50359862,"imageIndex":57},{"imageOffset":50343563,"imageIndex":57},{"imageOffset":85089,"symbol":"displayConfigFinalizedProc","symbolLocation":259,"imageIndex":163},{"imageOffset":44493,"symbol":"CGSPostLocalNotification","symbolLocation":220,"imageIndex":163},{"imageOffset":43232,"symbol":"(anonymous 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===== Log before crash start =====
Startup Messages
---
warning | QCoreApplication::postEvent: Unexpected null receiver
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/mosfe704/MHard/Postdoc_Uppsala/Practical/SAXS_ZC3/Process/Dammif/sub_001-1-1.cif
Summary of feedback from opening
/Users/mosfe704/MHard/Postdoc_Uppsala/Practical/SAXS_ZC3/Process/Dammif/sub_001-1-1.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
264 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for sub_001-1-1.cif #1
---
Chain | Description
A | No description available
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show cartoons
> open
> /Users/mosfe704/MHard/Postdoc_Uppsala/Practical/SAXS_ZC3/Process/Dammif/sub_001-1-1.cif
Summary of feedback from opening
/Users/mosfe704/MHard/Postdoc_Uppsala/Practical/SAXS_ZC3/Process/Dammif/sub_001-1-1.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
264 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for sub_001-1-1.cif #2
---
Chain | Description
A | No description available
> show #!2 target m
> close #2
> mlp
Map values for surface "sub_001-1-1.cif_A SES surface": minimum -2.649, mean
-2.376, maximum -2.118
To also show corresponding color key, enter the above mlp command and add key
true
> mlp
Map values for surface "sub_001-1-1.cif_A SES surface": minimum -2.649, mean
-2.376, maximum -2.118
To also show corresponding color key, enter the above mlp command and add key
true
> show cartoons
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> color byhetero
> color bychain
> color bypolymer
> rainbow
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A ASP 1
/A ASP 2
/A ASP 3
/A ASP 4
/A ASP 5
/A ASP 6
/A ASP 7
/A ASP 8
/A ASP 9
/A ASP 10
/A ASP 11
/A ASP 12
/A ASP 13
/A ASP 14
/A ASP 15
/A ASP 16
/A ASP 17
/A ASP 18
/A ASP 19
/A ASP 20
/A ASP 21
/A ASP 22
/A ASP 23
/A ASP 24
/A ASP 25
/A ASP 26
/A ASP 27
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for sub_001-1-1.cif_A SES surface #1.2: minimum, 0.40, mean
0.79, maximum 1.01
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic
Coulombic values for sub_001-1-1.cif_A SES surface #1.2: minimum, 0.40, mean
0.79, maximum 1.01
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic
Coulombic values for sub_001-1-1.cif_A SES surface #1.2: minimum, 0.40, mean
0.79, maximum 1.01
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp
Map values for surface "sub_001-1-1.cif_A SES surface": minimum -2.649, mean
-2.376, maximum -2.118
To also show corresponding color key, enter the above mlp command and add key
true
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style stick
Changed 269 atom styles
> style sphere
Changed 269 atom styles
> style ball
Changed 269 atom styles
> show surfaces
> hide surfaces
> show surfaces
> volume style surface
No volumes specified
> volume style surface
No volumes specified
> volume style surface
No volumes specified
> transparency 50
> transparency 0
> transparency 50
> volume showOutlineBox true
No volumes specified
> volume planes z style image imageMode "full region"
No volumes specified
> volume planes z style image imageMode "full region"
No volumes specified
> open "/Users/mosfe704/MHard/Postdoc_Uppsala/ZC3_Biophysical
> _manu/Results/AlphaFold3/fold_flzc3_zn (1)/fold_flzc3_zn_model_0.cif"
Summary of feedback from opening
/Users/mosfe704/MHard/Postdoc_Uppsala/ZC3_Biophysical
_manu/Results/AlphaFold3/fold_flzc3_zn (1)/fold_flzc3_zn_model_0.cif
---
note | Fetching CCD ZN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif
Chain information for fold_flzc3_zn_model_0.cif #2
---
Chain | Description
A | .
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> hide #1.2 models
> show #1.2 models
> hide #1.1 models
> hide #!1 models
> show #!1 models
> hide #2 models
> show #2 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> close #2
> open "/Users/mosfe704/MHard/Postdoc_Uppsala/ZC3_Biophysical
> _manu/Results/AlphaFold3/fold_flzc3_hsp70/fold_flzc3_hsp70_model_0.cif"
Chain information for fold_flzc3_hsp70_model_0.cif #2
---
Chain | Description
A | .
B | .
> open "/Users/mosfe704/MHard/Postdoc_Uppsala/ZC3_Biophysical
> _manu/Results/AlphaFold3/fold_flzc3_zn (1)/fold_flzc3_zn_model_0.cif"
Chain information for fold_flzc3_zn_model_0.cif #3
---
Chain | Description
A | .
> close #3
> open "/Users/mosfe704/MHard/Postdoc_Uppsala/ZC3_Biophysical
> _manu/Results/AlphaFold3/fold_flzc3_zn_hsp70/fold_flzc3_zn_hsp70_model_0.cif"
Chain information for fold_flzc3_zn_hsp70_model_0.cif #3
---
Chain | Description
A | .
B | .
> hide #!1 models
> hide #2 models
> show #2 models
> hide #1.2 models
> ui mousemode right "pick blobs"
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_flzc3_hsp70_model_0.cif, chain A (#2) with sub_001-1-1.cif,
chain A (#1), sequence alignment score = 22
Fewer than 3 residues aligned; cannot match fold_flzc3_hsp70_model_0.cif,
chain A with sub_001-1-1.cif, chain A
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #2-3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker sub_001-1-1.cif, chain A (#1) with fold_flzc3_hsp70_model_0.cif,
chain A (#2), sequence alignment score = 22
Fewer than 3 residues aligned; cannot match sub_001-1-1.cif, chain A with
fold_flzc3_hsp70_model_0.cif, chain A
Matchmaker sub_001-1-1.cif, chain A (#1) with fold_flzc3_zn_hsp70_model_0.cif,
chain A (#3), sequence alignment score = 61.8
Fewer than 3 residues aligned; cannot match sub_001-1-1.cif, chain A with
fold_flzc3_zn_hsp70_model_0.cif, chain A
> close #1
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #3 & sel to #2 & sel
No 'to' model specified
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show Matchmaker
> matchmaker #3 & sel to #2 & sel
No 'to' model specified
No reference and/or match structure/chain chosen
> matchmaker #3 & sel to #2 & sel
No 'to' model specified
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open
> /Users/mosfe704/MHard/Postdoc_Uppsala/Practical/SAXS_ZC3/Process/Dammif/sub_001-1-1.cif
Summary of feedback from opening
/Users/mosfe704/MHard/Postdoc_Uppsala/Practical/SAXS_ZC3/Process/Dammif/sub_001-1-1.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
264 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for sub_001-1-1.cif #1
---
Chain | Description
A | No description available
> mlp
Map values for surface "sub_001-1-1.cif_A SES surface": minimum -2.649, mean
-2.376, maximum -2.118
Map values for surface "fold_flzc3_zn_hsp70_model_0.cif_A SES surface":
minimum -29.45, mean -4.952, maximum 25.49
Map values for surface "fold_flzc3_zn_hsp70_model_0.cif_B SES surface":
minimum -29.48, mean -6.125, maximum 22.75
Map values for surface "fold_flzc3_hsp70_model_0.cif_A SES surface": minimum
-27.77, mean -4.274, maximum 22.64
Map values for surface "fold_flzc3_hsp70_model_0.cif_B SES surface": minimum
-29.85, mean -6.229, maximum 23.03
To also show corresponding color key, enter the above mlp command and add key
true
> select add #1
269 atoms, 26 pseudobonds, 27 residues, 2 models selected
> select subtract #1
1 model selected
> select add #1
269 atoms, 26 pseudobonds, 27 residues, 2 models selected
> select subtract #1
1 model selected
> select add #1
269 atoms, 26 pseudobonds, 27 residues, 2 models selected
> select subtract #1
1 model selected
> color byhetero
> color bychain
> color bypolymer
> rainbow
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
sub_001-1-1.cif #1/A ASP 1
sub_001-1-1.cif #1/A ASP 2
sub_001-1-1.cif #1/A ASP 3
sub_001-1-1.cif #1/A ASP 4
sub_001-1-1.cif #1/A ASP 5
sub_001-1-1.cif #1/A ASP 6
sub_001-1-1.cif #1/A ASP 7
sub_001-1-1.cif #1/A ASP 8
sub_001-1-1.cif #1/A ASP 9
sub_001-1-1.cif #1/A ASP 10
sub_001-1-1.cif #1/A ASP 11
sub_001-1-1.cif #1/A ASP 12
sub_001-1-1.cif #1/A ASP 13
sub_001-1-1.cif #1/A ASP 14
sub_001-1-1.cif #1/A ASP 15
sub_001-1-1.cif #1/A ASP 16
sub_001-1-1.cif #1/A ASP 17
sub_001-1-1.cif #1/A ASP 18
sub_001-1-1.cif #1/A ASP 19
sub_001-1-1.cif #1/A ASP 20
sub_001-1-1.cif #1/A ASP 21
sub_001-1-1.cif #1/A ASP 22
sub_001-1-1.cif #1/A ASP 23
sub_001-1-1.cif #1/A ASP 24
sub_001-1-1.cif #1/A ASP 25
sub_001-1-1.cif #1/A ASP 26
sub_001-1-1.cif #1/A ASP 27
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_flzc3_hsp70_model_0.cif_A SES surface #2.1: minimum,
-23.83, mean 0.22, maximum 23.63
Coulombic values for fold_flzc3_hsp70_model_0.cif_B SES surface #2.2: minimum,
-22.58, mean -2.44, maximum 11.68
Coulombic values for fold_flzc3_zn_hsp70_model_0.cif_A SES surface #3.1:
minimum, -20.39, mean -0.08, maximum 18.44
Coulombic values for fold_flzc3_zn_hsp70_model_0.cif_B SES surface #3.2:
minimum, -21.28, mean -2.33, maximum 11.60
Coulombic values for sub_001-1-1.cif_A SES surface #1.2: minimum, 0.40, mean
0.79, maximum 1.01
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp
Map values for surface "sub_001-1-1.cif_A SES surface": minimum -2.649, mean
-2.376, maximum -2.118
Map values for surface "fold_flzc3_zn_hsp70_model_0.cif_A SES surface":
minimum -29.45, mean -4.952, maximum 25.49
Map values for surface "fold_flzc3_zn_hsp70_model_0.cif_B SES surface":
minimum -29.48, mean -6.125, maximum 22.75
Map values for surface "fold_flzc3_hsp70_model_0.cif_A SES surface": minimum
-27.77, mean -4.274, maximum 22.64
Map values for surface "fold_flzc3_hsp70_model_0.cif_B SES surface": minimum
-29.85, mean -6.229, maximum 23.03
To also show corresponding color key, enter the above mlp command and add key
true
> show cartoons
> style stick
Changed 22604 atom styles
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!1 models
> hide #!3 models
> cartoon #2
> show #!2 cartoons
> hide #!2 cartoons
> hide #!2 models
> hide #3.1 models
> hide #3.2 models
> show #!3 models
> show #!2 models
> hide #2.2 models
> hide #2.1 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #3.1 models
> view #2 clip false
No displayed objects specified.
> hide #!2 models
> hide #3.1 models
> hide #!3 models
> show #!3 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!2 models
> hide #!2 models
> show #2.1 models
> hide #2.1 models
> hide #!2 models
> show #2.2 models
> hide #2.2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!2 surfaces
> show #!2 cartoons
> hide #!2 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> hide #!2 models
> show #!2 models
> hide #2.2 models
> show #!3 models
> select add #3
11169 atoms, 11333 bonds, 1454 residues, 1 model selected
> select subtract #3.1
4931 atoms, 5002 bonds, 644 residues, 3 models selected
> select subtract #3.2
3 atoms, 3 residues, 2 models selected
> select add #3
11169 atoms, 11333 bonds, 1454 residues, 1 model selected
> select add #2
22335 atoms, 22666 bonds, 2905 residues, 4 models selected
> ui tool show Matchmaker
> matchmaker #!2 & sel to #3 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_flzc3_zn_hsp70_model_0.cif, chain B (#3) with
fold_flzc3_hsp70_model_0.cif, chain B (#2), sequence alignment score = 3277.7
RMSD between 447 pruned atom pairs is 0.672 angstroms; (across all 641 pairs:
8.429)
> hide #!2 models
> show #!2 models
> select subtract #2
11169 atoms, 11333 bonds, 1454 residues, 5 models selected
> select subtract #3
2 models selected
> color #2 #ec363cff
> color #3 #887df6ff
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> color #1 #9275c9ff
> color #1 #bac924ff
> color #1 #c9c03eff
> color #1 #b5c91fff
> color #1 #c9c619ff
> show #!1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!1 models
> hide #!2 models
> show #!3 models
> close #3
> show #2.1 models
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #!1 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
No reference and/or match structure/chain chosen
> select down
Nothing selected
No reference and/or match structure/chain chosen
> matchmaker #!1 & sel to #2 & sel
No 'to' model specified
Alignment identifier is 2/A
Alignment identifier is 2/B
Alignment identifier is 1/A
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> ui mousemode right "mark surface"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 555 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro14,3
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2,8 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 529.120.1.0.0
OS Loader Version: 577.140.2~22
SMC Version (system): 2.45f5
Software:
System Software Overview:
System Version: macOS 13.6.7 (22G720)
Kernel Version: Darwin 22.6.0
Time since boot: 12 days, 27 minutes
Graphics/Displays:
Intel HD Graphics 630:
Chipset Model: Intel HD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x591b
Revision ID: 0x0004
Automatic Graphics Switching: Supported
gMux Version: 4.0.29 [3.2.8]
Metal Support: Metal 3
Radeon Pro 555:
Chipset Model: Radeon Pro 555
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 2 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c7
ROM Revision: 113-C980AJ-927
VBIOS Version: 113-C9801AP-A02
EFI Driver Version: 01.A0.927
Automatic Graphics Switching: Supported
gMux Version: 4.0.29 [3.2.8]
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
PHL 273V5:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: UK51801013981
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: Apple USB-C VGA Adapter
Adapter Firmware Version: 1,91
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 16 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash waking Mac up from sleep |
comment:2 by , 16 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash waking Mac up from sleep → Crash waking Mac up from sleep in displayConfigFinalizedProc, ATI graphics |
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Crash plugging in or unplugging an external display. Work-around code is not entirely reliable for old Mac machines with Intel or ATI graphics. Hoping Qt 6.7 or newer fixes this problem introduced in Qt 6.6.