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Opened 3 months ago
Closed 3 months ago
#18294 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-15.5-arm64-arm-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 0x0000000322c47000 (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 0x0000000321c3b000 (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 0x00000003151fb000 (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 0x00000003141ef000 (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 0x00000003131e3000 (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 0x00000003121d7000 (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 0x00000003111cb000 (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 0x00000003101bf000 (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 0x000000030f1b3000 (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 0x000000030e1a7000 (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 0x000000030d19b000 (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 0x0000000209d15f00 (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, lxml._elementpath, lxml.etree, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 64)
{"app_name":"ChimeraX","timestamp":"2025-07-24 22:44:53.00 +0200","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","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 15.5 (24F74)","roots_installed":0,"name":"ChimeraX","incident_id":"3F9ABC25-0DE8-4D12-83B1-2A9D1A9D6E9D"}
{
"uptime" : 470000,
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 3951,
"osVersion" : {
"train" : "macOS 15.5",
"build" : "24F74",
"releaseType" : "User"
},
"captureTime" : "2025-07-24 22:44:48.3581 +0200",
"codeSigningMonitor" : 1,
"incident" : "3F9ABC25-0DE8-4D12-83B1-2A9D1A9D6E9D",
"pid" : 86154,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-24 20:38:14.6491 +0200",
"procStartAbsTime" : 11143644153497,
"procExitAbsTime" : 11325887860810,
"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":"63CB1839-47F1-51AC-B97F-9F75A951AD0C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C0517820-33B7-C8B6-8F7E-8E9BCE6157A7",
"appleIntelligenceStatus" : {"reasons":["siriAssetIsNotReady","notOptedIn","assetIsNotReady"],"state":"unavailable"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "48B39E06-4F07-4037-A4C8-137334CC77BB",
"wakeTime" : 15722,
"sleepWakeUUID" : "FFDB9678-153A-48A3-9AD3-2FAE8441E692",
"sip" : "enabled",
"vmRegionInfo" : "0x35500000169 is not in any region. Bytes after previous region: 3182570766698 Bytes before following region: 101889509162647\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000035500000169","rawCodes":[1,3663607103849],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000035500000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":86154},
"vmregioninfo" : "0x35500000169 is not in any region. Bytes after previous region: 3182570766698 Bytes before following region: 101889509162647\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] 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" : 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===== Log before crash start =====
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
> open
> /Users/mccaff0001/Downloads/cryosparc_P331_J208_003_volume_map_sharp.mrc
Opened cryosparc_P331_J208_003_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.47, shown at level 0.155, step 1, values float32
> set bgColor white
> lighting soft intensity 0.1 direction 0.577,-0.577,-0.577 color 100,100,100
> fillIntensity 0.5 fillDirection -0.81,-1,1 fillColor 100,100,100
> ambientIntensity 1.4 ambientColor 100,100,100 shadows true qualityOfShadows
> finer depthBias 0.01 multiShadow 64 msMapSize 2000 msDepthBias 0.004
> moveWithCamera true
> open
> /Users/mccaff0001/Documents/PretzPaperFigs/pretzel1tetramer_flexfit_1.pdb
Summary of feedback from opening
/Users/mccaff0001/Documents/PretzPaperFigs/pretzel1tetramer_flexfit_1.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
54562 messages similar to the above omitted
Chain information for pretzel1tetramer_flexfit_1.pdb #2
---
Chain | Description
A B C D | No description available
> open /Users/mccaff0001/Documents/PretzPaperFigs/pretzel1tetramer_flexfit.pdb
Summary of feedback from opening
/Users/mccaff0001/Documents/PretzPaperFigs/pretzel1tetramer_flexfit.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU A 5 LEU A 13 1 9
Start residue of secondary structure not found: HELIX 2 2 LYS A 17 SER A 22 1
6
Start residue of secondary structure not found: HELIX 3 3 TYR A 29 THR A 42 1
14
Start residue of secondary structure not found: HELIX 4 4 ASP A 50 THR A 59 1
10
Start residue of secondary structure not found: HELIX 5 5 TYR A 69 LEU A 83 1
15
349 messages similar to the above omitted
Chain information for pretzel1tetramer_flexfit.pdb
---
Chain | Description
3.1/A 3.2/B 3.3/C 3.4/D | No description available
> hide atoms
> show cartoons
> color #1 #b2b2b272 models
> color #1 #b2b2b271 models
> graphics silhouettes true
> color #1 #b2b2b258 models
> color #1 #b2b2b248 models
> color #3.1 #7a81ffff
> color #2 #d783ffff
> open /Users/mccaff0001/Documents/PretzPaperFigs/structanalysis.cxs
opened ChimeraX session
> open /Users/mccaff0001/Documents/EMA2024poster/Posterstructs.cxs
Opened cryosparc_P880_J41_004_volume_map_sharp.mrc as #5, grid size
360,360,360, pixel 1.34, shown at level 0.243, step 2, values float32
Opened cryosparc_P331_J208_003_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.47, shown at level 0.155, step 1, values float32
opened ChimeraX session
> open /Users/mccaff0001/Documents/PretzPaperFigs/structanalysis.cxs
opened ChimeraX session
> open
> /Users/mccaff0001/Documents/PretzPaperFigs/Jul2025structurerendering.cxs
Opened cryosparc_J244_3-29A_volume_map_sharp.mrc as #2, grid size 420,420,420,
pixel 1.14, shown at level 0.279, step 1, values float32
Opened cryosparc_P331_J208_003_volume_map_sharp.mrc as #10, grid size
256,256,256, pixel 1.47, shown at level 0.155, step 1, values float32
opened ChimeraX session
> hide #!10 models
> show #!9 models
> hide #!11 models
> select add #9
72756 atoms, 74156 bonds, 40 pseudobonds, 8864 residues, 6 models selected
> transparency 0 sel target c
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency sel 0 target c
> select subtract #9
Nothing selected
> show #!10 models
> color #10 #a296a815 models
> color #10 #a296a814 models
> graphics silhouettes false
> graphics silhouettes true
> ui tool show "Side View"
> graphics silhouettes width 2
> color #10 #a296a859 models
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #9
72756 atoms, 74156 bonds, 40 pseudobonds, 8864 residues, 6 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap sel inMap #10
Fit molecules pretzel1tetramer_flexfit.pdb (#9.1),
pretzel1tetramer_flexfit.pdb (#9.2), pretzel1tetramer_flexfit.pdb (#9.3),
pretzel1tetramer_flexfit.pdb (#9.4) to map
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) using 72756 atoms
average map value = 0.1087, steps = 68
shifted from previous position = 3.34
rotated from previous position = 0.756 degrees
atoms outside contour = 49876, contour level = 0.15536
Position of pretzel1tetramer_flexfit.pdb (#9.1) relative to
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99682936 0.07775691 0.01688489 -33.02508314
-0.07737304 0.99675261 -0.02230855 22.17667973
-0.01856471 0.02093138 0.99960856 -3.50617310
Axis 0.26222078 0.21497770 -0.94075760
Axis point 270.06637423 433.73166700 0.00000000
Rotation angle (degrees) 4.72937574
Shift along axis -0.59391248
Position of pretzel1tetramer_flexfit.pdb (#9.2) relative to
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.99678828 0.07818631 0.01732188 363.73505443
-0.07733809 -0.99598125 0.04516848 384.19790383
0.02078383 0.04368377 0.99882922 -8.89086138
Axis -0.00954368 -0.02225331 -0.99970681
Axis point 189.39334630 185.11239622 0.00000000
Rotation angle (degrees) 175.53874086
Shift along axis -3.13278884
Position of pretzel1tetramer_flexfit.pdb (#9.3) relative to
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.99681676 0.07798291 -0.01658389 348.02558992
-0.07760709 -0.99673655 -0.02221279 391.34007402
-0.01826199 -0.02085505 0.99961574 10.48603193
Axis 0.00872553 0.01078432 -0.99990378
Axis point 181.68332105 188.94579438 0.00000000
Rotation angle (degrees) 175.53773625
Shift along axis -3.22797662
Position of pretzel1tetramer_flexfit.pdb (#9.4) relative to
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99683792 0.07775582 -0.01637718 -4.63989303
-0.07695040 0.99601385 0.04511172 3.83788227
0.01981959 -0.04370884 0.99884772 1.67639540
Axis -0.48795644 -0.19885537 -0.84991473
Axis point 46.90616564 61.10264465 0.00000000
Rotation angle (degrees) 5.22187472
Shift along axis 0.07608901
> fitmap sel inMap #10
Fit molecules pretzel1tetramer_flexfit.pdb (#9.1),
pretzel1tetramer_flexfit.pdb (#9.2), pretzel1tetramer_flexfit.pdb (#9.3),
pretzel1tetramer_flexfit.pdb (#9.4) to map
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) using 72756 atoms
average map value = 0.1087, steps = 48
shifted from previous position = 0.0271
rotated from previous position = 0.0106 degrees
atoms outside contour = 49889, contour level = 0.15536
Position of pretzel1tetramer_flexfit.pdb (#9.1) relative to
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99683971 0.07765722 0.01673204 -32.98005985
-0.07727702 0.99676060 -0.02228415 22.17316519
-0.01840836 0.02092072 0.99961168 -3.51982748
Axis 0.26242125 0.21343860 -0.94105210
Axis point 270.43732120 433.63280935 0.00000000
Rotation angle (degrees) 4.72191423
Shift along axis -0.60971825
Position of pretzel1tetramer_flexfit.pdb (#9.2) relative to
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.99678400 0.07827590 0.01716262 363.74588073
-0.07743406 -0.99597269 0.04519290 384.23265262
0.02063102 0.04371859 0.99883087 -8.85124017
Axis -0.00946555 -0.02226822 -0.99970722
Axis point 189.40784289 185.12070943 0.00000000
Rotation angle (degrees) 175.53340923
Shift along axis -3.15058120
Position of pretzel1tetramer_flexfit.pdb (#9.3) relative to
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.99680641 0.07808258 -0.01673676 348.03272064
-0.07770395 -0.99672948 -0.02219162 391.37374414
-0.01841480 -0.02082024 0.99961366 10.52305405
Axis 0.00880211 0.01077036 -0.99990326
Axis point 181.69777831 188.95401101 0.00000000
Rotation angle (degrees) 175.53208614
Shift along axis -3.24337881
Position of pretzel1tetramer_flexfit.pdb (#9.4) relative to
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99684227 0.07766624 -0.01653643 -4.59389962
-0.07685350 0.99602037 0.04513288 3.83723220
0.01997592 -0.04371948 0.99884414 1.66756063
Axis -0.48834543 -0.20067721 -0.84926285
Axis point 46.93537934 60.69808257 0.00000000
Rotation angle (degrees) 5.21957720
Shift along axis 0.05716757
> select subtract #9
Nothing selected
> select add #9
72756 atoms, 74156 bonds, 40 pseudobonds, 8864 residues, 6 models selected
> fitmap sel inMap #10
Fit molecules pretzel1tetramer_flexfit.pdb (#9.1),
pretzel1tetramer_flexfit.pdb (#9.2), pretzel1tetramer_flexfit.pdb (#9.3),
pretzel1tetramer_flexfit.pdb (#9.4) to map
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) using 72756 atoms
average map value = 0.1087, steps = 48
shifted from previous position = 0.0203
rotated from previous position = 0.0212 degrees
atoms outside contour = 49884, contour level = 0.15536
Position of pretzel1tetramer_flexfit.pdb (#9.1) relative to
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99682764 0.07787535 0.01643511 -32.96015739
-0.07750174 0.99674364 -0.02226226 22.20436317
-0.01811527 0.02091789 0.99961709 -3.56279832
Axis 0.26181669 0.20949129 -0.94210691
Axis point 270.02339677 432.15329709 0.00000000
Rotation angle (degrees) 4.73012785
Shift along axis -0.62136149
Position of pretzel1tetramer_flexfit.pdb (#9.2) relative to
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.99680738 0.07803906 0.01688110 363.84876696
-0.07720928 -0.99598915 0.04521467 384.17445465
0.02034191 0.04376694 0.99883468 -8.78762015
Axis -0.00932254 -0.02228556 -0.99970818
Axis point 189.43492039 185.11008032 0.00000000
Rotation angle (degrees) 175.54668182
Shift along axis -3.16847911
Position of pretzel1tetramer_flexfit.pdb (#9.3) relative to
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.99681844 0.07786442 -0.01703367 348.13155661
-0.07748017 -0.99674755 -0.02216221 391.31957812
-0.01870391 -0.02077192 0.99960930 10.58190162
Axis 0.00894879 0.01075081 -0.99990216
Axis point 181.72547125 188.94451160 0.00000000
Rotation angle (degrees) 175.54478163
Shift along axis -3.25850920
Position of pretzel1tetramer_flexfit.pdb (#9.4) relative to
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99681908 0.07790308 -0.01681797 -4.57963907
-0.07707724 0.99600175 0.04516223 3.86217786
0.02026900 -0.04372229 0.99883812 1.63334870
Axis -0.48712221 -0.20325124 -0.84935321
Axis point 47.13203375 60.34467732 -0.00000000
Rotation angle (degrees) 5.23462021
Shift along axis 0.05856150
> fitmap sel inMap #10
Fit molecules pretzel1tetramer_flexfit.pdb (#9.1),
pretzel1tetramer_flexfit.pdb (#9.2), pretzel1tetramer_flexfit.pdb (#9.3),
pretzel1tetramer_flexfit.pdb (#9.4) to map
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) using 72756 atoms
average map value = 0.1087, steps = 48
shifted from previous position = 0.0327
rotated from previous position = 0.0156 degrees
atoms outside contour = 49871, contour level = 0.15536
Position of pretzel1tetramer_flexfit.pdb (#9.1) relative to
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99682294 0.07787815 0.01670457 -33.01005736
-0.07749969 0.99674476 -0.02221949 22.18454624
-0.01838061 0.02085430 0.99961358 -3.52819453
Axis 0.26103605 0.21262338 -0.94162173
Axis point 269.65349060 432.93252118 0.00000000
Rotation angle (degrees) 4.73259318
Shift along axis -0.57763726
Position of pretzel1tetramer_flexfit.pdb (#9.2) relative to
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.99680164 0.07805369 0.01715016 363.79641279
-0.07721124 -0.99598705 0.04525741 384.15554048
0.02061385 0.04378847 0.99882816 -8.87542717
Axis -0.00945805 -0.02230170 -0.99970655
Axis point 189.41022499 185.10191268 0.00000000
Rotation angle (degrees) 175.54619765
Shift along axis -3.13530208
Position of pretzel1tetramer_flexfit.pdb (#9.3) relative to
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.99682323 0.07786166 -0.01676421 348.08440277
-0.07748380 -0.99674822 -0.02211953 391.30144718
-0.01843196 -0.02075031 0.99961480 10.49802432
Axis 0.00881320 0.01073470 -0.99990354
Axis point 181.70046898 188.93582213 0.00000000
Rotation angle (degrees) 175.54476280
Shift along axis -3.22877140
Position of pretzel1tetramer_flexfit.pdb (#9.4) relative to
cryosparc_P331_J208_003_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99682473 0.07788845 -0.01654891 -4.62808742
-0.07707355 0.99600011 0.04520487 3.84266359
0.02000365 -0.04378585 0.99884068 1.66108761
Axis -0.48789582 -0.20040115 -0.84958640
Axis point 46.89857636 60.85081381 0.00000000
Rotation angle (degrees) 5.23255911
Shift along axis 0.07671290
> select subtract #9
Nothing selected
> save /Users/mccaff0001/Documents/PretzPaperFigs/structinmap.png width 3000
> height 3916 supersample 3 transparentBackground true
> close session
> open /Users/mccaff0001/Downloads/I7MLD7/fold_2024_07_03_13_51_model_0.cif
Chain information for fold_2024_07_03_13_51_model_0.cif #1
---
Chain | Description
A | .
> open /Users/mccaff0001/Downloads/I7MGF4_unrelaxed_model_1.pdb
Chain information for I7MGF4_unrelaxed_model_1.pdb #2
---
Chain | Description
A | No description available
> open /Users/mccaff0001/Downloads/I7M9Z0_unrelaxed_model_1.pdb
Chain information for I7M9Z0_unrelaxed_model_1.pdb #3
---
Chain | Description
A | No description available
> mmaker #2 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 fold_2024_07_03_13_51_model_0.cif, chain A (#1) with
I7MGF4_unrelaxed_model_1.pdb, chain A (#2), sequence alignment score = 3662.9
RMSD between 500 pruned atom pairs is 1.171 angstroms; (across all 1805 pairs:
21.064)
> mmaker #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 fold_2024_07_03_13_51_model_0.cif, chain A (#1) with
I7M9Z0_unrelaxed_model_1.pdb, chain A (#3), sequence alignment score = 4273.6
RMSD between 165 pruned atom pairs is 1.266 angstroms; (across all 2138 pairs:
22.020)
===== 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
> open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain1.pdb
Chain information for CMAC_Domain1.pdb #1
---
Chain | Description
A | No description available
> open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain2.pdb
Chain information for CMAC_Domain2.pdb #2
---
Chain | Description
A | No description available
> open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain3.pdb
Chain information for CMAC_Domain3.pdb #3
---
Chain | Description
A | No description available
> open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain4.pdb
Chain information for CMAC_Domain4.pdb #4
---
Chain | Description
A | No description available
> open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain5.pdb
Chain information for CMAC_Domain5.pdb #5
---
Chain | Description
A | No description available
> open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain6.pdb
Chain information for CMAC_Domain6.pdb #6
---
Chain | Description
A | No description available
> open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain7.pdb
Chain information for CMAC_Domain7.pdb #7
---
Chain | Description
A | No description available
> open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain8.pdb
Chain information for CMAC_Domain8.pdb #8
---
Chain | Description
A | No description available
> open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain9.pdb
Chain information for CMAC_Domain9.pdb #9
---
Chain | Description
A | No description available
> open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain10.pdb
Chain information for CMAC_Domain10.pdb #10
---
Chain | Description
A | No description available
> open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain11.pdb
Chain information for CMAC_Domain11.pdb #11
---
Chain | Description
A | No description available
> open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain12.pdb
Chain information for CMAC_Domain12.pdb #12
---
Chain | Description
A | No description available
> open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain13.pdb
Chain information for CMAC_Domain13.pdb #13
---
Chain | Description
A | No description available
> open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain14.pdb
Chain information for CMAC_Domain14.pdb #14
---
Chain | Description
A | No description available
> open /Users/mccaff0001/Downloads/DomainPDBs/CMAC_Domain15.pdb
Chain information for CMAC_Domain15.pdb #15
---
Chain | Description
A | No description available
> set bgColor white
> lighting soft intensity 0.1 direction 0.577,-0.577,-0.577 color 100,100,100
> fillIntensity 0.5 fillDirection -0.81,-1,1 fillColor 100,100,100
> ambientIntensity 1.4 ambientColor 100,100,100 shadows true qualityOfShadows
> finer depthBias 0.01 multiShadow 64 msMapSize 2000 msDepthBias 0.004
> moveWithCamera true
> select add #8
834 atoms, 848 bonds, 104 residues, 1 model selected
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> hide #1 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.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: Mac14,7
Model Number: Z16S000YASM/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 20 days, 15 hours, 37 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
24B1W:
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: 0.7.16
annotated-types: 0.7.0
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-ArtiaX: 0.6.0
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
geomdl: 5.3.1
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
pandas: 2.2.3
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
pyarrow: 19.0.1
pycollada: 0.8
pydantic: 2.11.3
pydantic-core: 2.33.1
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
starfile: 0.5.12
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
typing-inspection: 0.4.0
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 , 3 months 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 , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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