![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Closed 13 months ago
#16213 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-14.6.1-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 0x00000001eef48f40 (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, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath (total: 54)
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{
"uptime" : 1100000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,12",
"coalitionID" : 1632,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2024-10-29 12:11:39.7148 -0400",
"codeSigningMonitor" : 1,
"incident" : "7AC392A5-198E-4A4A-8FCB-C0D25A7527E7",
"pid" : 32113,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-10-29 10:04:58.3101 -0400",
"procStartAbsTime" : 26588448558614,
"procExitAbsTime" : 26770866720301,
"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":"4ED9390D-1A59-5781-A84C-5FF0F7298AEB","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "6FDE2CF6-FF50-54FD-9B72-86671C3480FD",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 9619,
"sleepWakeUUID" : "7281EC93-ADD2-4A86-B5FD-242441B25F4B",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4305256087\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1009d0000-1009d4000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":32113},
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 4305256087\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1009d0000-1009d4000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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"name" : "fcntl.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_sha512.cpython-311-darwin.so",
"name" : "_sha512.cpython-311-darwin.so"
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"uuid" : "1eab426b-5d06-3a22-b7b5-6dbc112704d6",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_random.cpython-311-darwin.so",
"name" : "_random.cpython-311-darwin.so"
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"uuid" : "a97f3cfd-a5a7-3ce2-9eb6-5ebc0943bd1d",
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"uuid" : "65172ede-2b95-337d-970f-ed6c4a217cb1",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/zlib.cpython-311-darwin.so",
"name" : "zlib.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_typing.cpython-311-darwin.so",
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"uuid" : "3b2e1e73-f5e1-3fa3-80b3-e46009060893",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_datetime.cpython-311-darwin.so",
"name" : "_datetime.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/math.cpython-311-darwin.so",
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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/fanyanglv/Library/CloudStorage/OneDrive-
> McMasterUniversity/RhsP2 writing/RhsP2 writing/alforld/Toxic plus
> NAD/DT_plus_nad/fold_dt_plus_nad_model_0.cif"
Chain information for fold_dt_plus_nad_model_0.cif #1
---
Chain | Description
A | .
> open "/Users/fanyanglv/Library/CloudStorage/OneDrive-
> McMasterUniversity/RhsP2 writing/RhsP2 writing/alforld/Toxic plus
> NAD/fold_ctdoxin_plus_nad/fold_ctdoxin_plus_nad_model_0.cif"
Chain information for fold_ctdoxin_plus_nad_model_0.cif #2
---
Chain | Description
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 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_dt_plus_nad_model_0.cif, chain A (#1) with
fold_ctdoxin_plus_nad_model_0.cif, chain A (#2), sequence alignment score =
26.2
RMSD between 4 pruned atom pairs is 0.800 angstroms; (across all 71 pairs:
18.468)
> hide #1 models
> select add #2
1561 atoms, 1614 bonds, 191 residues, 1 model selected
Alignment identifier is 2/A
> select #2/A:3
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:3-6
36 atoms, 36 bonds, 4 residues, 1 model selected
> select #2/A:5
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:5
11 atoms, 10 bonds, 1 residue, 1 model selected
> show #1 models
> hide #2 models
> select #2/A:1-2
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A
1517 atoms, 1566 bonds, 190 residues, 1 model selected
> hide #1 atoms
> undo
> select #2/A:1-2
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A
1517 atoms, 1566 bonds, 190 residues, 1 model selected
> hide #1 atoms
> show #1 atoms
> undo
> select #2/A:190
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:190
12 atoms, 11 bonds, 1 residue, 1 model selected
> select add #1
1489 atoms, 1519 bonds, 188 residues, 2 models selected
> select subtract #1
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:1-2
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:1-25
196 atoms, 199 bonds, 25 residues, 1 model selected
> select #2/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:1-71
560 atoms, 571 bonds, 71 residues, 1 model selected
> select add #2
1561 atoms, 1614 bonds, 191 residues, 1 model selected
> show #2 models
> select subtract #2
Nothing selected
> hide #2 models
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
> select #1/A:9
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:9
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:2-186
1425 atoms, 1452 bonds, 185 residues, 1 model selected
> select #1/A:186
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A
1433 atoms, 1460 bonds, 186 residues, 1 model selected
> select #1/A:186
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:186
5 atoms, 4 bonds, 1 residue, 1 model selected
> open "/Users/fanyanglv/Library/CloudStorage/OneDrive-
> McMasterUniversity/RhsP2 writing/RhsP2 writing/alforld/Toxic plus
> NAD/fold_rhsp2_plus_nad/fold_rhsp2_plus_nad_model_0.cif"
Chain information for fold_rhsp2_plus_nad_model_0.cif #3
---
Chain | Description
A | .
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 #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 fold_dt_plus_nad_model_0.cif, chain A (#1) with
fold_ctdoxin_plus_nad_model_0.cif, chain A (#2), sequence alignment score =
26.2
RMSD between 4 pruned atom pairs is 0.800 angstroms; (across all 71 pairs:
18.468)
Matchmaker fold_dt_plus_nad_model_0.cif, chain A (#1) with
fold_rhsp2_plus_nad_model_0.cif, chain A (#3), sequence alignment score = 32.9
RMSD between 14 pruned atom pairs is 1.401 angstroms; (across all 106 pairs:
14.244)
> hide #3 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A
1433 atoms, 1460 bonds, 186 residues, 1 model selected
> color sel dark gray
> select #1/A:186
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:186
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A
1433 atoms, 1460 bonds, 186 residues, 1 model selected
> color sel light gray
> select #1/A:12
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:12
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:10-13,16-21,51-54,77-82,86-91,131-137,145-149,158-164
354 atoms, 353 bonds, 45 residues, 1 model selected
> select #1/A:8
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:8-173
1286 atoms, 1311 bonds, 166 residues, 1 model selected
> hide sel atoms
> select #1/A:19
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:19
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:16
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:16-22
54 atoms, 55 bonds, 7 residues, 1 model selected
> select #1/A:16-22,49-55
111 atoms, 113 bonds, 14 residues, 1 model selected
> select #1/A:16-22,49-58
140 atoms, 143 bonds, 17 residues, 1 model selected
> select #1/A:144-145
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A:144-147
34 atoms, 34 bonds, 4 residues, 1 model selected
> select #1/A:16-21,144-147
79 atoms, 80 bonds, 10 residues, 1 model selected
> select #1/A:16-21,50-58,144-147
156 atoms, 159 bonds, 19 residues, 1 model selected
> ui tool show "Color Actions"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color sel orange
> color sel #ffbc55ff
> color sel #f6ca46ff
> color sel #f6cb48ff
> color sel #f6ca46ff
> color sel #f67880ff
> color sel #f6777fff
> color sel #f6ca46ff
> select #1/A:144
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:144-147
34 atoms, 34 bonds, 4 residues, 1 model selected
> color sel #f5c946ff
> select #1/A:19
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:19
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:19,63-64
28 atoms, 28 bonds, 3 residues, 1 model selected
> select #1/A:58
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:58
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:52
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:52
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:52,146
21 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #1/A:19,52,146
31 atoms, 30 bonds, 3 residues, 1 model selected
> color sel byhetero
> select #1/A:186
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:186
5 atoms, 4 bonds, 1 residue, 1 model selected
> save image.png supersample 4 transparentBackground true
> select clear
> save image.png supersample 4 transparentBackground true
> lighting flat
> lighting soft
> lighting simple
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> graphics silhouettes false
> lighting simple
> ui tool show "Side View"
> lighting simple
> lighting shadows true
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> graphics silhouettes false
> lighting simple
> set bgColor white
> save image.png supersample 4 transparentBackground true
> hide #1 models
> show #2 models
> ui tool show "Side View"
> lighting simple
> ui tool show "Side View"
Alignment identifier is 1/A
Alignment identifier is 2/A
Alignment identifier is 3/A
> select #2/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A
1517 atoms, 1566 bonds, 190 residues, 1 model selected
> color sel gray
> color sel light gray
> select add #2
1561 atoms, 1614 bonds, 191 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #cab28fff
> color sel #cab290ff
> color sel #c9b18fff
> color sel #c8b18fff
> color sel #c8b08eff
> color sel #c7b08eff
> color sel #c7af8dff
> color sel #c6af8dff
> color sel #c6ae8dff
> color sel #c5ae8cff
> color sel #c5ad8cff
> color sel #c4ad8cff
> color sel #c4ad8bff
> color sel #c3ac8bff
> color sel #c2ab8aff
> color sel #c1aa89ff
> color sel #c0a989ff
> color sel #c0a988ff
> color sel #bfa888ff
> color sel #bea887ff
> color sel #bea787ff
> color sel #bda787ff
> color sel #bda786ff
> color sel #bda686ff
> color sel #bca686ff
> color sel #bda686ff
> color sel #bda787ff
> color sel #bea787ff
> color sel #bea887ff
> color sel #bfa888ff
> color sel #bfa988ff
> color sel #c0a989ff
> color sel #c1aa89ff
> color sel #c1aa8aff
> color sel #c2ab8aff
> color sel #c3ac8bff
> color sel #c4ac8bff
> color sel #c4ad8bff
> color sel #c5ad8cff
> color sel #c5ae8cff
> color sel #c6ae8dff
> color sel #c6af8dff
> color sel #c7af8dff
> color sel #c7b08eff
> color sel #c8b08eff
> color sel #c9b18fff
> color sel #cab28fff
> color sel #cab290ff
> color sel #cbb290ff
> color sel #cbb390ff
> color sel #cbb391ff
> color sel #ccb491ff
> color sel #cdb492ff
> color sel #cdb592ff
> color sel #ceb592ff
> color sel #cfb693ff
> color sel #cfb793ff
> color sel #d0b794ff
> color sel #d0b894ff
> color sel #d1b895ff
> color sel #d1b995ff
> color sel #d2b995ff
> color sel #d2b996ff
> color sel #d2ba96ff
> color sel #d3ba96ff
> color sel #d3ba97ff
> color sel #d4bb97ff
> color sel #f7dcb1ff
> color sel #f2d5abff
> color sel byhetero
> select subtract #2
Nothing selected
> select #2/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A
1517 atoms, 1566 bonds, 190 residues, 1 model selected
> color sel light gray
> select #2/A:1-2
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:1-6
53 atoms, 53 bonds, 6 residues, 1 model selected
> select #2/A:8-9
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:1-9
78 atoms, 78 bonds, 9 residues, 1 model selected
> select #2/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:1-6
53 atoms, 53 bonds, 6 residues, 1 model selected
> select #2/A:9
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:8-9
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:7
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:2-7
53 atoms, 53 bonds, 6 residues, 1 model selected
> select #2/A:2-7,55-60
97 atoms, 97 bonds, 12 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #f6ca46ff
> select #2/A:106-107
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/A:106-110
42 atoms, 42 bonds, 5 residues, 1 model selected
> select #2/A:105
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:105-110
52 atoms, 53 bonds, 6 residues, 1 model selected
> select #2/A:108-109
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #2/A:108-111
34 atoms, 33 bonds, 4 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #f6ca46ff
> select #2/A:10-11
14 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/A:10-102
724 atoms, 741 bonds, 93 residues, 1 model selected
> select #2/A:2-3
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:2-12
92 atoms, 94 bonds, 11 residues, 1 model selected
> hide sel atoms
> select #2/A:56
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:56-64
64 atoms, 64 bonds, 9 residues, 1 model selected
> hide sel atoms
> select #2/A:95
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:95-152
482 atoms, 497 bonds, 58 residues, 1 model selected
> hide sel atoms
> select #2/A:8-48
325 atoms, 331 bonds, 41 residues, 1 model selected
> select #2/A:8-181
1396 atoms, 1441 bonds, 174 residues, 1 model selected
> hide sel atoms
> undo
> hide sel atoms
> select #2/A:5
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:5
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:5,59
17 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/A:5,59,110
26 atoms, 23 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero
> hide sel atoms
> select clear
> select #2/A:188
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:188-190
24 atoms, 24 bonds, 3 residues, 1 model selected
> hide sel cartoons
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting simple
> save image.png supersample 4 transparentBackground true
> select #2/A:5-6
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/A:5-6
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/A:5-6
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/A:5
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:5
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:5,59
17 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/A:5,59,110
26 atoms, 23 bonds, 3 residues, 1 model selected
> show sel atoms
> select clear
> ui tool show "Side View"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save image.png supersample 4 transparentBackground true
> hide #2 models
> show #1 models
Alignment identifier is 1/A
Alignment identifier is 2/A
Alignment identifier is 3/A
> select #3/A:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:8-97
705 atoms, 720 bonds, 90 residues, 1 model selected
> select #1/A:3
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:3-85
634 atoms, 650 bonds, 83 residues, 1 model selected
> hide sel atoms
> select #1/A:88
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:88-180
733 atoms, 743 bonds, 93 residues, 1 model selected
> hide sel atoms
> select clear
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> ui tool show "Side View"
> lighting simple
> save image.png supersample 4 transparentBackground true
===== 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/fanyanglv/Library/CloudStorage/OneDrive-
> McMasterUniversity/RhsP2 writing/RhsP2 writing/alforld/Toxic plus
> NAD/fold_ctdoxin_plus_nad/fold_ctdoxin_plus_nad_model_0.cif"
Chain information for fold_ctdoxin_plus_nad_model_0.cif #1
---
Chain | Description
A | .
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3
OpenGL vendor: Apple
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 Air
Model Identifier: Mac15,12
Model Number: Z1BD000MLLL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 39 days, 14 hours, 49 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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 , 13 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 , 13 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
We believe this crash is fixed in the ChimeraX daily build and 1.9 release candidates. It is a bug in the Qt window toolkit that ChimeraX uses that sometimes causes crashes when plugging in or unplugging an external display or when waking from sleep.
Crash in Qt 6.6 in _NSViewHierarchyDidChangeBackingProperties.
Note:
See TracTickets
for help on using tickets.
Reported by Fanyang Lyu