![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#16885 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-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001e2ea5000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix (total: 56)
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"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 2343,
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"build" : "23C71",
"releaseType" : "User"
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"captureTime" : "2025-02-18 14:27:09.8310 +0000",
"codeSigningMonitor" : 1,
"incident" : "4C4295A0-31B7-41B1-892C-A6DC169DC232",
"pid" : 71790,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-18 13:04:04.9415 +0000",
"procStartAbsTime" : 7448226745982,
"procExitAbsTime" : 7567856383681,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"1F17ACA8-7311-5748-B4F1-E589D374643B","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "929905E1-EC35-CE0E-F5BA-59B708505CA1",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 100889,
"sleepWakeUUID" : "2C69F20F-6339-4375-9508-0AC1BC0A97B5",
"sip" : "enabled",
"vmRegionInfo" : "0x4c1f8d91d768 is not in any region. Bytes after previous region: 83217366505321 Bytes before following region: 21854713424024\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00004c1f8d91d768","rawCodes":[1,83698402842472],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00004c1f8d91d768"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":71790},
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/weilongzhao/Desktop/HisCC_1longHelix2actins_IsoldeFitted_realspace_refined.pdb
Chain information for
HisCC_1longHelix2actins_IsoldeFitted_realspace_refined.pdb #1
---
Chain | Description
D E | No description available
k | No description available
> set bgColor white
> lighting full
> lighting soft
> graphics silhouettes true
Drag select of 18 residues
> select up
637 atoms, 656 bonds, 72 residues, 1 model selected
> select up
5800 atoms, 5926 bonds, 742 residues, 1 model selected
> select clear
> open
> /Users/weilongzhao/Downloads/fold_2024_05_08_16_12_drebrin_hel_cc_factin/fold_2024_05_08_16_12_drebrin_hel_cc_factin_model_0.cif
Chain information for fold_2024_05_08_16_12_drebrin_hel_cc_factin_model_0.cif
#2
---
Chain | Description
A | .
B C D E F G | .
> close #1
> show cartoons
Computing secondary structure
> hide atoms
Drag select of 585 residues
> select up
6480 atoms, 6573 bonds, 833 residues, 1 model selected
> select up
17550 atoms, 17928 bonds, 2250 residues, 1 model selected
> color sel gray
> select clear
> color byattribute seq_conservation
No known/registered numeric attribute seq_conservation
> open
> /Users/weilongzhao/Downloads/mus_xeno_danio_anolis_gallus_full_length_alignment.fasta
Summary of feedback from opening
/Users/weilongzhao/Downloads/mus_xeno_danio_anolis_gallus_full_length_alignment.fasta
---
notes | Alignment identifier is mus_xeno_danio_anolis_gallus_full_length_alignment.fasta
Associated fold_2024_05_08_16_12_drebrin_hel_cc_factin_model_0.cif chain A to
AF-Q16643-F1-model_v4.pdb (#0) chain A/1-649 with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment mus_xeno_danio_anolis_gallus_full_length_alignment.fasta
Opened 6 sequences from
mus_xeno_danio_anolis_gallus_full_length_alignment.fasta
> color byattribute seq_conservation
19570 atoms, 2482 residues, atom seq_conservation range -1.81 to 1.21
> select clear
> select /A:3
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:3-4
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:33
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:33-42
81 atoms, 80 bonds, 10 residues, 1 model selected
> select /A:32-33
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /A:32-38
51 atoms, 50 bonds, 7 residues, 1 model selected
> select /A:28
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:28-59
283 atoms, 286 bonds, 32 residues, 1 model selected
> select /A:28
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:28-86
532 atoms, 536 bonds, 59 residues, 1 model selected
> open
> /Users/weilongzhao/Desktop/HisCC_1longHelix2actins_IsoldeFitted_realspace_refined.pdb
Chain information for
HisCC_1longHelix2actins_IsoldeFitted_realspace_refined.pdb #1
---
Chain | Description
D E | No description available
k | No description available
Associated HisCC_1longHelix2actins_IsoldeFitted_realspace_refined.pdb chain k
to AF-Q16643-F1-model_v4.pdb (#0) chain A/1-649 with 0 mismatches
> close #1
> select clear
> ui tool show "Side View"
> save "/Users/weilongzhao/Documents/University/PhD/Lab
> Meeting/20250218/CC_Hel_AF3_conservation.jpg" width 1344 height 786
> supersample 3
> save "/Users/weilongzhao/Documents/University/PhD/Lab
> Meeting/20250218/Hel_AF3_conservation.jpg" width 1344 height 786 supersample
> 3
> hide #2 models
> open
> /Users/weilongzhao/Desktop/HisCC_1longHelix2actins_IsoldeFitted_realspace_refined.pdb
Chain information for
HisCC_1longHelix2actins_IsoldeFitted_realspace_refined.pdb #1
---
Chain | Description
D E | No description available
k | No description available
Associated HisCC_1longHelix2actins_IsoldeFitted_realspace_refined.pdb chain k
to AF-Q16643-F1-model_v4.pdb (#0) chain A/1-649 with 0 mismatches
> color #1 bychain
> select ::name="ADP"
54 atoms, 58 bonds, 2 residues, 1 model selected
> color sel byhetero
> select ::name="MG"
8 atoms, 8 residues, 2 models selected
> color (#1 & sel) lime
> select clear
> select #1/k:48
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
437 atoms, 440 bonds, 47 residues, 1 model selected
> select up
615 atoms, 620 bonds, 67 residues, 1 model selected
> select up
6471 atoms, 6604 bonds, 813 residues, 1 model selected
> select down
615 atoms, 620 bonds, 67 residues, 1 model selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/k
Alignment identifier is 1/k
> select #1/k:92
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/k:90-92
32 atoms, 32 bonds, 3 residues, 1 model selected
> select #1/k:33-39,42-92
534 atoms, 537 bonds, 58 residues, 1 model selected
> select clear
> select #1/k:94
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/k:94
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/k:56
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/k:56
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #1/k:42
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/k:42
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #1/k:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/k:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #1/k:86
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/k:86
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #1/k:33-39,42-92
534 atoms, 537 bonds, 58 residues, 1 model selected
> select #1/k:75
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/k:75
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> save "/Users/weilongzhao/Documents/University/PhD/Lab
> Meeting/20250218/HisCC_model_R42R56.jpg" width 1344 height 786 supersample 3
> ui tool show "Show Sequence Viewer"
> sequence chain #1/D #1/E
Alignment identifier is 1
> select #1/D-E:334
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/D-E:334
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel cartoons
> show sel atoms
> color sel byhetero
> select clear
> select #1/D-E:293
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/D-E:292-293
32 atoms, 30 bonds, 4 residues, 1 model selected
> select
> #1/D-E:56-60,62-64,79-93,98-100,113-126,137-145,172-174,182-196,203-216,223-232,252-254,258-261,264-267,274-283,290-294,303-305,309-320,338-348,359-373
2582 atoms, 2596 bonds, 316 residues, 1 model selected
> select #1/D-E:292
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/D-E:292
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> open /Users/weilongzhao/Downloads/cryosparc_P123_J182_map_sharp.mrc
Opened cryosparc_P123_J182_map_sharp.mrc as #3, grid size 448,448,448, pixel
0.85, shown at level 0.0023, step 2, values float32
> volume #3 step 1
> volume #3 level 0.2271
> volume #3 color #b2b2b299
> select clear
> volume #3 level 0.09775
> save "/Users/weilongzhao/Documents/University/PhD/Lab
> Meeting/20250218/HisCC_model_R42R56.jpg" width 1344 height 786 supersample 3
> volume #3 level 0.1255
> select #1/D-E:335
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/D-E:335-336
40 atoms, 38 bonds, 4 residues, 1 model selected
> select #1/D-E:335
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/D-E:335
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #1/D-E:336
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/D-E:336
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/D-E:334
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/D-E:334
18 atoms, 16 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #1/D-E:311
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/D-E:311
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> volume #3 level 0.1255
> save "/Users/weilongzhao/Documents/University/PhD/Lab
> Meeting/20250218/HisCC_model_E79R86.jpg" width 1344 height 786 supersample 3
> hide #1 models
> show #2 models
> hide #2 models
> hide #!3 models
> open /Users/weilongzhao/Desktop/isolde_fitted_Hel_1actin7bvr.pdb
Chain information for isolde_fitted_Hel_1actin7bvr.pdb #4
---
Chain | Description
A | No description available
B | No description available
Associated isolde_fitted_Hel_1actin7bvr.pdb chain A to
AF-Q16643-F1-model_v4.pdb (#0) chain A/1-649 with 0 mismatches
> color #!4 bychain
> open /Users/weilongzhao/Downloads/cryosparc_P123_J184_map_sharp.mrc
Opened cryosparc_P123_J184_map_sharp.mrc as #5, grid size 448,448,448, pixel
0.85, shown at level 0.00237, step 2, values float32
> volume #5 level 0.09248
> volume #5 step 1
> volume #5 color darkgrey
> select ::name="ADP"
93 atoms, 99 bonds, 3 residues, 2 models selected
> color sel & #!4 byhetero
> select clear
Drag select of 10 residues
> select up
523 atoms, 523 bonds, 32 residues, 1 model selected
> select up
5776 atoms, 5839 bonds, 371 residues, 1 model selected
> select down
523 atoms, 523 bonds, 32 residues, 1 model selected
> select up
5776 atoms, 5839 bonds, 371 residues, 1 model selected
> select up
5816 atoms, 5880 bonds, 373 residues, 1 model selected
> select up
6261 atoms, 6328 bonds, 401 residues, 1 model selected
> select down
5816 atoms, 5880 bonds, 373 residues, 1 model selected
> select up
6261 atoms, 6328 bonds, 401 residues, 1 model selected
> select up
32302 atoms, 32914 bonds, 3696 residues, 7 models selected
> select down
6261 atoms, 6328 bonds, 401 residues, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> select clear
> select ::name="ADP"
93 atoms, 99 bonds, 3 residues, 2 models selected
> show sel & #!4 cartoons
> show sel & #!4 atoms
> select ::name="MG"
9 atoms, 9 residues, 3 models selected
> show sel & #!4 atoms
> color (#!4 & sel) lime
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/D #1/E #4/B
Alignment identifier is 2
> select #1/D-E:151 #4/B:151
35 atoms, 32 bonds, 3 residues, 2 models selected
> select #1/D-E:151-244 #4/B:151-244
2944 atoms, 2980 bonds, 282 residues, 2 models selected
2 [ID: 2] region chains B,D,E [147-240] RMSD: 0.425
> select #1/D-E:333 #4/B:333
28 atoms, 28 bonds, 3 residues, 2 models selected
> select #1/D-E:333-375 #4/B:333-375
1400 atoms, 1430 bonds, 129 residues, 2 models selected
2 [ID: 2] region chains B,D,E [329-371] RMSD: 0.489
> select #1/D-E:375 #4/B:375
45 atoms, 45 bonds, 3 residues, 2 models selected
> select #1/D-E:370-375 #4/B:370-375
221 atoms, 224 bonds, 18 residues, 2 models selected
2 [ID: 2] region chains B,D,E [366-371] RMSD: 0.427
> select #1/D-E:5-49 #4/B:5-49
1265 atoms, 1280 bonds, 135 residues, 2 models selected
> select #1/D-E:5-375 #4/B:5-375
11576 atoms, 11765 bonds, 1113 residues, 2 models selected
2 [ID: 2] region chains B,D,E [1-371] RMSD: 0.452
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A #4/A
Alignment identifier is 2
> select #2/A:101
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:101-149 #4/A:139-149
553 atoms, 554 bonds, 60 residues, 2 models selected
. [ID: 2] region 2 chains [101-149] RMSD: 357.034
> select #2/A:1-138,167-220
1601 atoms, 1624 bonds, 192 residues, 1 model selected
> select #2/A:110
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:110
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:153 #4/A:153
20 atoms, 18 bonds, 2 residues, 2 models selected
> select #2/A:153 #4/A:153
20 atoms, 18 bonds, 2 residues, 2 models selected
. [ID: 2] region 2 chains [153] RMSD: 381.731
> select #1/D-E:70
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/D-E:70-71
30 atoms, 30 bonds, 4 residues, 1 model selected
> select #1/D-E:54-99
772 atoms, 794 bonds, 92 residues, 1 model selected
> select #1/D-E:54-101
810 atoms, 834 bonds, 96 residues, 1 model selected
> select #1/D-E:103
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/D-E:103-205
1596 atoms, 1626 bonds, 206 residues, 1 model selected
> select #1/D-E:61
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/D-E:61-158
1572 atoms, 1612 bonds, 196 residues, 1 model selected
> select #2/A:1-2
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #2/A:1-210 #4/A
2195 atoms, 2225 bonds, 238 residues, 2 models selected
. [ID: 2] region 2 chains [1-210] RMSD: 369.697
> select clear
> select #4/A:146
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
121 atoms, 120 bonds, 9 residues, 1 model selected
> select up
445 atoms, 448 bonds, 28 residues, 1 model selected
> select clear
> select #2/A:1-210 #4/A
2195 atoms, 2225 bonds, 238 residues, 2 models selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A #4/A
Alignment identifier is 1
> select #2/A:197
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:197-199
22 atoms, 23 bonds, 3 residues, 1 model selected
> select #2/A:11-57
404 atoms, 409 bonds, 47 residues, 1 model selected
> select #2/A:11-205 #4/A
2095 atoms, 2124 bonds, 223 residues, 2 models selected
. [ID: 1] region 2 chains [11-205] RMSD: 369.697
> select #2/A:52
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:52-145 #4/A:139-145
928 atoms, 932 bonds, 101 residues, 2 models selected
. [ID: 2] region 2 chains [52-145] RMSD: 351.884
> ui tool show "Show Sequence Viewer"
> sequence chain #1/D #1/E #4/B
Alignment identifier is 1
> sequence chain #2/A #4/A
Alignment identifier is 3
> select #2/A:60
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:60-156 #4/A:139-156
1119 atoms, 1127 bonds, 115 residues, 2 models selected
. [ID: 3] region 2 chains [60-156] RMSD: 364.877
> select clear
> select #1/D-E:60 #4/B:60
23 atoms, 20 bonds, 3 residues, 2 models selected
> select #1/D-E:60-244 #4/B:60-244
5897 atoms, 5996 bonds, 555 residues, 2 models selected
1 [ID: 1] region chains B,D,E [56-240] RMSD: 0.432
> select clear
> select #1/D-E:332 #4/B:332
28 atoms, 28 bonds, 3 residues, 2 models selected
> select #1/D-E:332 #4/B:332
28 atoms, 28 bonds, 3 residues, 2 models selected
1 [ID: 1] region chains B,D,E [328] RMSD: 0.266
> select #4/A:146
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
121 atoms, 120 bonds, 9 residues, 1 model selected
> select up
445 atoms, 448 bonds, 28 residues, 1 model selected
> select #2/A:156 #4/A:156
35 atoms, 33 bonds, 2 residues, 2 models selected
> select #2/A:156 #4/A:156
35 atoms, 33 bonds, 2 residues, 2 models selected
. [ID: 3] region 2 chains [156] RMSD: 370.753
> show sel & #!4 atoms
> style sel & #!4 stick
Changed 24 atom styles
> color sel & #!4 byhetero
> select #2/A:163 #4/A:163
24 atoms, 22 bonds, 2 residues, 2 models selected
> select #2/A:163 #4/A:163
24 atoms, 22 bonds, 2 residues, 2 models selected
. [ID: 3] region 2 chains [163] RMSD: 374.885
> show sel & #!4 cartoons
> show sel & #!4 atoms
> color sel & #!4 byhetero
> select H
3106 atoms, 400 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #1/D-E:24 #4/B:24
24 atoms, 21 bonds, 3 residues, 2 models selected
> select #1/D-E:24 #4/B:24
24 atoms, 21 bonds, 3 residues, 2 models selected
1 [ID: 1] region chains B,D,E [20] RMSD: 0.910
> show sel & #!4 atoms
> style sel & #!4 stick
Changed 8 atom styles
> color sel & #!4 byhetero
> select #1/D-E:344 #4/B:344
18 atoms, 15 bonds, 3 residues, 2 models selected
> select #1/D-E:344 #4/B:344
18 atoms, 15 bonds, 3 residues, 2 models selected
1 [ID: 1] region chains B,D,E [340] RMSD: 0.335
> show sel & #!4 atoms
> style sel & #!4 stick
Changed 6 atom styles
> color sel & #!4 byhetero
> select #1/D-E:350 #4/B:350
18 atoms, 15 bonds, 3 residues, 2 models selected
> select #1/D-E:350-351 #4/B:350-351
39 atoms, 36 bonds, 6 residues, 2 models selected
1 [ID: 1] region chains B,D,E [346-347] RMSD: 0.628
> show sel & #!4 atoms
> style sel & #!4 stick
Changed 13 atom styles
> color sel & #!4 byhetero
> select clear
> show #!5 models
> color #5 #a9a9a9a8 models
> color #5 #a9a9a9a1 models
> color #5 #a9a9a999 models
> select clear
> save "/Users/weilongzhao/Documents/University/PhD/Lab
> Meeting/20250218/HelHis_model_R156E163.jpg" width 1344 height 786
> supersample 3
> hide #!4 models
> hide #!5 models
> open 8VO5
Summary of feedback from opening 8VO5 fetched from pdb
---
note | Fetching compressed mmCIF 8vo5 from http://files.rcsb.org/download/8vo5.cif
8vo5 title:
Cryo-EM structure of fascin bound to F-actin (actin binding site 1) [more
info...]
Chain information for 8vo5 #6
---
Chain | Description | UniProt
A | Fascin | FSCN1_HUMAN 1-493
B C D | Actin, alpha skeletal muscle | ACTS_CHICK 3-375
Non-standard residues in 8vo5 #6
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
> ui tool show "Side View"
> color #!6 bychain
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> close #6
> show #!5 models
> show #!3 models
> color #3 #b2b2b2ff models
> color #5 darkgrey models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> ui tool show "Color Zone"
> hide #!5 models
> color zone #3 near #1 distance 5.1
> color zone #5 near #4 distance 5.1
> show #!5 models
> volume #5 level 0.1342
> open /Users/weilongzhao/Desktop/isolde_fitted_Hel_1actin7bvr.pdb
Chain information for isolde_fitted_Hel_1actin7bvr.pdb #6
---
Chain | Description
A | No description available
B | No description available
Associated isolde_fitted_Hel_1actin7bvr.pdb chain A to
AF-Q16643-F1-model_v4.pdb (#0) chain A/1-649 with 0 mismatches
> open /Users/weilongzhao/Desktop/isolde_fitted_Hel_1actin7bvr.pdb
Chain information for isolde_fitted_Hel_1actin7bvr.pdb #7
---
Chain | Description
A | No description available
B | No description available
Associated isolde_fitted_Hel_1actin7bvr.pdb chain A to
AF-Q16643-F1-model_v4.pdb (#0) chain A/1-649 with 0 mismatches
> hide #!7 models
> show #!7 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: MLY33B/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 8 days, 1 hour, 46 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
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: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
ChimeraX-Clipper: 0.24.0
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.9
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 8 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 , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
When you reported this ChimeraX crash it explained in the Report a Bug panel what we know about it:
"This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX."
We have updated Qt in the ChimeraX daily build to Qt 6.8.2 that might fix this Qt bug. You could try the daily build.