![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 months ago
Closed 3 months ago
#18374 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
Current thread 0x00000001ef6adf00 (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, PIL._imagingmath, 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, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 54)
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{
"uptime" : 240000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,6",
"coalitionID" : 3262,
"osVersion" : {
"train" : "macOS 15.5",
"build" : "24F74",
"releaseType" : "User"
},
"captureTime" : "2025-08-04 10:26:29.3507 -0400",
"codeSigningMonitor" : 1,
"incident" : "9DE56445-1212-4386-BCAB-65F0C70B179D",
"pid" : 10185,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-08-04 08:57:36.2901 -0400",
"procStartAbsTime" : 5857684427410,
"procExitAbsTime" : 5985677471420,
"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":"8A0DEBBA-E629-56FE-A554-9DB986703AD3","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "999B5ACF-7899-A575-EB8B-89F6BAD982ED",
"appleIntelligenceStatus" : {"state":"available"},
"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" : "825016ED-E003-4E43-BEB2-75E8C899CDF8",
"wakeTime" : 7636,
"sleepWakeUUID" : "624B0FE6-7E62-4F83-897F-E2F2B55FD0EF",
"sip" : "enabled",
"vmRegionInfo" : "0x2815b0a418c8 is not in any region. Bytes after previous region: 43592586631369 Bytes before following region: 61479493297976\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, 0x0000a815b0a418c8","rawCodes":[1,184811111323848],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000a815b0a418c8 -> 0x00002815b0a418c8 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":10185},
"vmregioninfo" : "0x2815b0a418c8 is not in any region. Bytes after previous region: 43592586631369 Bytes before following region: 61479493297976\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 ",
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"faultingThread" : 0,
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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/ehecatlga/work/Fitted_tutorial/1hkw_docking/1hkw_cluster_40ns_docking/rep.c0.pdb
> format pdb
Chain information for rep.c0.pdb #1
---
Chain | Description
? | No description available
> select add #1
13310 atoms, 13435 bonds, 891 residues, 1 model selected
> show sel surfaces
> ui mousemode right select
> select clear
> select /?:448
19 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
> select /?:447
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select clear
> select /?:448
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color cornflower blue
> color byhetero
> undo
> color byhetero
> undo
> hide surfaces
> color byhetero
> show surfaces
> color byhetero
> color bychain
> undo
> hide surfaces
> undo
> show surfaces
> color byhetero
> hide #!1 models
> show #!1 models
> color #1 #0096ffff
> color #1 #0433ffff
> color #1 #011993ff
> color #1 #0096ffff
> color #1 #009193ff
> color #1 #009051ff
> select #1/?: UNL
48 atoms, 48 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> color light sea green
> color cornflower blue
> select #1/?: UNL
48 atoms, 48 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select #1/?
13310 atoms, 13435 bonds, 891 residues, 1 model selected
> transparency 60
> transparency 40
> tranparency 70
Unknown command: tranparency 70
> transparency 70
> select up
13310 atoms, 13435 bonds, 891 residues, 2 models selected
> select up
13310 atoms, 13435 bonds, 891 residues, 2 models selected
> select up
13310 atoms, 13435 bonds, 891 residues, 2 models selected
> select up
13310 atoms, 13435 bonds, 891 residues, 2 models selected
> select #1/?: UNL
48 atoms, 48 bonds, 1 residue, 1 model selected
> color sel orange
> color sel byhetero
> color sel #f1fff4ff
> color sel #f0fff4ff
> color sel #eefff4ff
> color sel #eafff5ff
> color sel #e7fff5ff
> color sel #e3fff5ff
> color sel #e1fff5ff
> color sel #dffff5ff
> color sel #ddfff5ff
> color sel #dafff5ff
> color sel #d6fff5ff
> color sel #d0fff5ff
> color sel #c9fff5ff
> color sel #c1fff5ff
> color sel #bbfff5ff
> color sel #b5fff5ff
> color sel #affff5ff
> color sel #abfff5ff
> color sel #a5fff5ff
> color sel #9ffff6ff
> color sel #9afff7ff
> color sel #95fff9ff
> color sel #90fffaff
> color sel #8bfffcff
> color sel #86fffeff
> color sel #80fdffff
> color sel #7bfaffff
> color sel #76f7ffff
> color sel #71f4ffff
> color sel #6df1ffff
> color sel #69efffff
> color sel #67edffff
> color sel #66ecffff
> color sel #6eefffff
> color sel #7ef5ffff
> color sel #94fcffff
> color sel #acfffaff
> color sel #c4fff3ff
> color sel #d8ffebff
> color sel #e2ffe1ff
> color sel #f1ffe0ff
> color sel #fbffd9ff
> color sel #fffcd2ff
> color sel #fff8ccff
> color sel #fff4c7ff
> color sel #fff1c2ff
> color sel #ffeebdff
> color sel #ffebb8ff
> color sel #ffe7b3ff
> color sel #ffe3aeff
> color sel #ffdfa8ff
> color sel #ffdaa2ff
> color sel #ffd59cff
> color sel #ffd097ff
> color sel #ffcb91ff
> color sel #ffc68bff
> color sel #ffc286ff
> color sel #ffbe80ff
> color sel #ffba7bff
> color sel #ffb776ff
> color sel #ffb371ff
> color sel #ffb06cff
> color sel #ffad67ff
> color sel #ffab64ff
> color sel #ffaa61ff
> color sel #ffaa60ff
> color sel #ffa95fff
> color sel #ffa95eff
> color sel #ffa95cff
> color sel #ffa859ff
> color sel #ffa756ff
> color sel #ffa653ff
> color sel #ffa54fff
> color sel #ffa34cff
> color sel #ffa349ff
> color sel #ffa247ff
> color sel #ffa146ff
> color sel #ffa145ff
> color sel #ffa042ff
> color sel #ff9f3fff
> color sel #ff9f3dff
> color sel #ff9f3aff
> color sel #ff9f39ff
> color sel #ffa037ff
> color sel #ffa236ff
> color sel #ffa335ff
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> color sel byhetero
> select clear
> hide atoms
> select #1/?: UNL
48 atoms, 48 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> set bgColor white
> select #1/?:
Expected an objects specifier or a keyword
> select #1/?
13310 atoms, 13435 bonds, 891 residues, 1 model selected
> transparency 0
> select clear
> lighting full
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> select clear
> open /Users/ehecatlga/work/clusters_trial/cluster_400ns/rep.c1.pdb
Chain information for rep.c1.pdb #2
---
Chain | Description
? | No description available
> 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 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 rep.c0.pdb, chain (blank) (#1) with rep.c1.pdb, chain (blank) (#2),
sequence alignment score = 4262.5
RMSD between 724 pruned atom pairs is 1.058 angstroms; (across all 890 pairs:
1.810)
> hide #!1 models
> hide #2 atoms
> select #2/?
13310 atoms, 13435 bonds, 891 residues, 1 model selected
> show sel surfaces
> color (#!2 & sel) byhetero
> undo
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> select #2/?
13310 atoms, 13435 bonds, 891 residues, 1 model selected
> select #2/?: UNL
48 atoms, 48 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> color sel byhetero
> color sel #dcb6ffff
> color sel #debbffff
> color sel #e5c8ffff
> color sel #efdcffff
> color sel #fbf4ffff
> color sel #fcfff6ff
> color sel #f3ffe5ff
> color sel #edffd9ff
> color sel #e9ffd0ff
> color sel #e6ffcaff
> color sel #e4ffc6ff
> color sel #e3ffc4ff
> color sel #e2ffc3ff
> color sel #e2ffc2ff
> color sel #e1ffc0ff
> color sel #dfffbdff
> color sel #d7ffb0ff
> color sel #d0ffa7ff
> color sel #c8ff9dff
> color sel #c1ff93ff
> color sel #baff89ff
> color sel #b4ff80ff
> color sel #afff7aff
> color sel #acff75ff
> color sel #aaff71ff
> color sel #a8ff6eff
> color sel #a7ff6aff
> color sel #a5ff67ff
> color sel #a3ff64ff
> color sel #a2ff61ff
> color sel #a0ff5eff
> color sel #9fff5bff
> color sel #9eff58ff
> color sel #9cff56ff
> color sel #9bff53ff
> color sel #9aff50ff
> color sel #98ff4eff
> color sel #97ff4bff
> color sel #95ff47ff
> color sel #92ff44ff
> color sel #90ff41ff
> color sel #8eff3eff
> color sel #8bff3bff
> color sel #88ff37ff
> color sel #85ff34ff
> color sel #82ff31ff
> color sel #7fff2fff
> color sel #7dff2dff
> color sel #7bff2bff
> color sel #79ff2aff
> color sel #77ff28ff
> color sel #75ff27ff
> color sel #73ff25ff
> color sel #71ff24ff
> color sel #6fff22ff
> color sel #6dff21ff
> color sel #6bff20ff
> color sel #69ff1fff
> color sel #68ff1eff
> color sel #66ff1eff
> color sel #65ff1dff
> color sel #64ff1cff
> color sel #63ff1bff
> color sel #62ff1bff
> color sel #61ff1aff
> color sel #60ff1aff
> color sel #5fff1aff
> color sel #5eff1aff
> color sel #5dff19ff
> color sel #5bff19ff
> color sel #59ff19ff
> color sel #57ff18ff
> color sel #56ff18ff
> color sel #55ff18ff
> color sel #55ff19ff
> color sel #56ff1bff
> color sel #5dff1bff
> color sel #5cff1aff
> color sel #5dff1dff
> color sel #62ff21ff
> color sel #68ff26ff
> color sel #70ff2bff
> color sel #77ff30ff
> color sel #7dff34ff
> color sel #86ff39ff
> color sel #88ff3cff
> color sel #8bff3eff
> color sel #8dff40ff
> color sel #8fff42ff
> color sel #92ff45ff
> color sel #95ff49ff
> color sel #98ff4dff
> color sel #9bff50ff
> color sel #9eff53ff
> color sel #a3ff59ff
> color sel #a5ff5bff
> color sel #a7ff5eff
> color sel #a9ff60ff
> color sel #abff64ff
> color sel #aeff67ff
> color sel #afff6aff
> color sel #b1ff6dff
> color sel #b2ff6fff
> color sel #b3ff72ff
> color sel #b5ff76ff
> color sel #b7ff79ff
> color sel #b9ff7dff
> color sel #baff80ff
> color sel #bcff83ff
> color sel #bdff85ff
> color sel #bdff87ff
> color sel #bdff89ff
> color sel #bdff8aff
> color sel #bcff8bff
> color sel #bcff8cff
> color sel #bcff8dff
> color sel #bbff8eff
> color sel #baff8eff
> color sel #b9ff8eff
> color sel #b7ff8eff
> color sel #b6ff8eff
> color sel #b3ff8eff
> color sel #b1ff8dff
> color sel #aeff8cff
> color sel #abff8bff
> color sel #a7ff89ff
> color sel #a2ff87ff
> color sel #9fff86ff
> color sel #9dff84ff
> color sel #9aff83ff
> color sel #97ff81ff
> color sel #93ff80ff
> color sel #90ff7eff
> color sel #8dff7dff
> color sel #8bff7cff
> color sel #89ff7cff
> color sel #88ff7bff
> color sel #87ff7bff
> color sel #86ff7bff
> color sel #86ff7cff
> color sel #85ff7dff
> color sel #85ff7eff
> color sel #84ff7eff
> color sel #84ff7fff
> color sel #84ff80ff
> color sel #83ff76ff
> color sel #85ff77ff
> color sel #88ff78ff
> color sel #8cff79ff
> color sel #90ff7aff
> color sel #93ff7bff
> color sel #95ff7cff
> color sel #98ff7cff
> color sel #9dff7eff
> color sel #9fff7eff
> color sel #a1ff7eff
> color sel #a2ff7fff
> color sel #a4ff80ff
> color sel #a7ff82ff
> color sel #adff87ff
> color sel #b0ff8aff
> color sel #b3ff8eff
> color sel #b9ff96ff
> color sel #bbff9aff
> color sel #bdff9dff
> color sel #bfffa0ff
> color sel #c1ffa2ff
> color sel #c2ffa5ff
> color sel #c4ffa7ff
> color sel #c5ffa9ff
> color sel #c9ffadff
> color sel #caffaeff
> color sel #cbffafff
> color sel #cbffaeff
> color sel #caffadff
> color sel #c9ffadff
> color sel #c8ffabff
> color sel #c6ffa9ff
> color sel #c4ffa7ff
> color sel #c2ffa4ff
> color sel #bfffa2ff
> color sel #bdff9fff
> color sel #bbff9bff
> color sel #b9ff98ff
> color sel #b7ff95ff
> color sel #b3ff90ff
> color sel #b1ff8dff
> color sel #afff8aff
> color sel #aeff88ff
> color sel #acff86ff
> color sel #abff83ff
> color sel #a9ff80ff
> color sel #a8ff7dff
> color sel #a5ff77ff
> color sel #a3ff74ff
> color sel #a2ff72ff
> color sel #a1ff70ff
> color sel #a1ff6fff
> color sel #a0ff6eff
> color sel #9fff6dff
> color sel #9fff6cff
> color sel #a0ff6bff
> color sel #a0ff6cff
> color sel #a1ff6dff
> color sel #a0ff6dff
> color sel #9fff6dff
> color sel #9eff6dff
> color sel #9eff6eff
> color sel #9dff6eff
> color sel #9dff6fff
> color sel #9dff70ff
> color sel byhetero
> select clear
> select #2/?: UNL
48 atoms, 48 bonds, 1 residue, 1 model selected
> color sel #f1ffa5ff
> color sel #f2ffa5ff
> color sel #f3ffa4ff
> color sel #f7ffa3ff
> color sel #fcffa7ff
> color sel #ffffaaff
> color sel #fff9b4ff
> color sel #fff3bfff
> color sel #ffefc5ff
> color sel #ffeacbff
> color sel #ffe8cdff
> color sel #ffe7ceff
> color sel #ffe6cfff
> color sel #ffe7d0ff
> color sel #ffe7d2ff
> color sel #ffe7d5ff
> color sel #ffe8d7ff
> color sel #ffe8d9ff
> color sel #ffe8dbff
> color sel #ffe8dcff
> color sel #ffeadbff
> color sel #f1ddcfff
> color sel #f0dcceff
> color sel #efdbcdff
> color sel #ead7c9ff
> color sel #e6d3c6ff
> color sel #e4d1c4ff
> color sel #e2cfc2ff
> color sel #deccbfff
> color sel #d3c2b6ff
> color sel #d0beb2ff
> color sel #c8b8acff
> color sel #c5b4a9ff
> color sel #c1b1a6ff
> color sel #bdada2ff
> color sel #bbaca1ff
> color sel #bbaba1ff
> color sel #bbaba0ff
> color sel #bcaca1ff
> color sel #bfafa4ff
> color sel #c5b4a9ff
> color sel #cebdb1ff
> color sel #d8c6baff
> color sel #edd9ccff
> color sel #f5e1d3ff
> color sel #fce7d9ff
> color sel #ffeadbff
> color sel #ffe7d4ff
> color sel #ffe8d3ff
> color sel #fff0d2ff
> color sel #fff6d3ff
> color sel #fffcd4ff
> color sel #f1ffd0ff
> color sel #e9ffceff
> color sel #e1ffc9ff
> color sel #d8ffc4ff
> color sel #c9ffbaff
> color sel #c3ffb5ff
> color sel #baffaeff
> color sel #b7ffacff
> color sel #b5ffabff
> color sel #b3ffa9ff
> color sel #aeffa5ff
> color sel #acffa3ff
> color sel #a5ff9eff
> color sel #a2ff9cff
> color sel #9dff97ff
> color sel #98ff93ff
> color sel #96ff92ff
> color sel #95ff90ff
> color sel #94ff8fff
> color sel #93ff8eff
> color sel #93fe8eff
> color sel #8bf187ff
> color sel #89ee85ff
> color sel #87ea83ff
> color sel #83e47fff
> color sel #81e07dff
> color sel #7ed979ff
> color sel #7bd677ff
> color sel #79d275ff
> color sel #77ce73ff
> color sel #75cb71ff
> color sel #71c46eff
> color sel #6ebf6aff
> color sel #6cbc69ff
> color sel #6bb967ff
> color sel #68b364ff
> color sel #66b163ff
> color sel #65af62ff
> color sel #64ae61ff
> color sel #63ac60ff
> color sel #62aa5fff
> color sel #61a85eff
> color sel #60a65dff
> color sel #5fa55cff
> color sel #5ea35bff
> color sel #5da25aff
> color sel #5da15aff
> color sel #5c9f59ff
> color sel #5b9e58ff
> color sel #5a9d57ff
> color sel #5a9c57ff
> color sel #599b56ff
> color sel #599a56ff
> color sel #599956ff
> color sel #589955ff
> color sel #599956ff
> color sel #599a56ff
> color sel #5a9c57ff
> color sel #5a9d57ff
> color sel #5b9d58ff
> color sel #5ea35bff
> color sel #61a85eff
> color sel #69b665ff
> color sel #6dbc69ff
> color sel #73c86fff
> color sel #76cc72ff
> color sel #79d275ff
> color sel #7ad476ff
> color sel #7bd577ff
> color sel #7bd677ff
> color sel #7cd778ff
> color sel #7cd878ff
> color sel #7dd979ff
> color sel #7fdb7aff
> color sel #7fdc7bff
> color sel #80de7cff
> color sel #85e680ff
> color sel #87eb83ff
> color sel #8af086ff
> color sel #8df589ff
> color sel #91fa8cff
> color sel #93ff8eff
> color sel forest green
> color sel byhetero
> select clear
> select #2/?:447
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/?:448
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> ui tool show "Side View"
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
===== 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 "/Volumes/TOSHIBA
> EXT/Rorqual_July_2025/filtering_eigthround/filtered_poses.sdf"
> hide #1.1-124 target m
> show #1.1 models
> hide #1.1 models
> show #1.2 models
> show #1.1 models
> hide #1.2 models
> select add #1.1
43 atoms, 44 bonds, 1 residue, 1 model selected
> select subtract #1.1
Nothing selected
> hide #1.1 models
> show #1.3 models
> hide #1.3 models
> show #1.4 models
> hide #1.4 models
> show #1.5 models
> hide #1.5 models
> show #1.1 models
> hide #1.1 models
> show #1.37 models
> hide #1.37 models
> show #1.49 models
> hide #1.49 models
> show #1.53 models
> hide #1.53 models
> show #1.95 models
> hide #1.95 models
> show #1.2 models
> open
> /Users/ehecatlga/work/Fitted_tutorial/1hkw_docking/1hkw_cluster_40ns_docking/1hkw1_cluster1_process_prepare/cluster_c1_correct_dummy_pro.mol2
Chain information for cluster_c1_correct_dummy_pro.mol2 #2
---
Chain | Description
? | No description available
Opened cluster_c1_correct_dummy_pro.mol2 containing 1 structure (13335 atoms,
13456 bonds)
> hide #1.2 models
> show #1.1 models
> select add #1.1
43 atoms, 44 bonds, 1 residue, 1 model selected
> select sel @< 5
5907 atoms, 6144 bonds, 146 residues, 125 models selected
> show sel & #2#1.1 atoms
> ui mousemode right select
> select clear
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3 Pro
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: Mac15,6
Model Number: MRX33LL/A
Chip: Apple M3 Pro
Total Number of Cores: 11 (5 performance and 6 efficiency)
Memory: 18 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: 23 days, 56 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL S2409W:
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
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 , 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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