![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 weeks ago
Closed 4 weeks ago
#19098 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-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 0x00000001e0fa5000 (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.surface._surface, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath (total: 55)
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{
"uptime" : 3800000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,3",
"coalitionID" : 339939,
"osVersion" : {
"train" : "macOS 14.2",
"build" : "23C64",
"releaseType" : "User"
},
"captureTime" : "2025-10-10 14:32:26.0386 +0200",
"codeSigningMonitor" : 1,
"incident" : "9B75C73D-AD20-4B11-B623-CD70D4673CC9",
"pid" : 52885,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-10-09 14:58:59.6659 +0200",
"procStartAbsTime" : 90521269610205,
"procExitAbsTime" : 91210432115734,
"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":"B37B9A4F-3C95-5B11-BACD-1BDB3DB05CC4","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "0C748E25-7680-0375-14CE-AD2C31BE7E26",
"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" : 1,
"sleepWakeUUID" : "459380F2-54C6-4E40-BB8C-02F6B83063EC",
"sip" : "enabled",
"vmRegionInfo" : "0x5001c5628638 is not in any region. Bytes after previous region: 87487500420665 Bytes before following region: 17584579508680\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, 0x0000d001c5628638","rawCodes":[1,228706025113144],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000d001c5628638 -> 0x00005001c5628638 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":52885},
"vmregioninfo" : "0x5001c5628638 is not in any region. Bytes after previous region: 87487500420665 Bytes before following region: 17584579508680\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 ",
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"faultingThread" : 0,
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===== Log before crash start =====
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/janpetrovsky/Desktop/RNA_POL_2/backup_maps/cryosparc_P8_J2067_007_volume_map
> (7).mrc"
Opened cryosparc_P8_J2067_007_volume_map (7).mrc as #1, grid size 250,250,250,
pixel 1.12, shown at level 0.117, step 1, values float32
> open
> /Users/janpetrovsky/Desktop/rnapol_p4a_isolda/final_model/isolda_phenix_7.pdb
Chain information for isolda_phenix_7.pdb #2
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
Q | No description available
T | No description available
> select add #2
64621 atoms, 65383 bonds, 31 pseudobonds, 3978 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> select ::name="B4P"
77 atoms, 82 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /T:31
32 atoms, 33 bonds, 1 residue, 1 model selected
> select up
1204 atoms, 1297 bonds, 38 residues, 1 model selected
> color sel blue
> select clear
> select /Q:2
34 atoms, 36 bonds, 1 residue, 1 model selected
> select up
260 atoms, 279 bonds, 8 residues, 1 model selected
> select up
64621 atoms, 65383 bonds, 3978 residues, 1 model selected
> select down
260 atoms, 279 bonds, 8 residues, 1 model selected
> color sel red
> select clear
> surface dust #1 size 11.2
> open "/Users/janpetrovsky/Downloads/cryosparc_P8_J2925_004_volume_map
> (1).mrc"
Opened cryosparc_P8_J2925_004_volume_map (1).mrc as #3, grid size 256,256,256,
pixel 1.52, shown at level 0.0714, step 1, values float32
> surface dust #1 size 11.2
> surface dust #3 size 15.2
> select #3
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.38511,-0.30274,-0.87181,522.15,0.92278,-0.13966,-0.35912,95.325,-0.013038,-0.94279,0.33314,315.48
> view matrix models
> #3,-0.99303,-0.071487,-0.093717,461.07,-0.11205,0.8192,0.56246,-45.461,0.036565,0.56904,-0.8215,220.79
> volume #3 level 0.1504
> volume #1 level 0.1134
> volume #3 level 0.1472
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.99303,-0.071487,-0.093717,383.48,-0.11205,0.8192,0.56246,-94.454,0.036565,0.56904,-0.8215,174.91
> view matrix models
> #3,-0.99303,-0.071487,-0.093717,366.38,-0.11205,0.8192,0.56246,-103.91,0.036565,0.56904,-0.8215,180.9
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.99526,-0.090571,-0.035479,359.69,-0.093868,0.79861,0.59448,-109.63,-0.025508,0.59499,-0.80333,185.29
> view matrix models
> #3,-0.95436,-0.29277,-0.058994,395.69,-0.2778,0.79775,0.53519,-59.957,-0.10962,0.52715,-0.84267,223.68
> fitmap #3 inMap #1
Fit map cryosparc_P8_J2925_004_volume_map (1).mrc in map
cryosparc_P8_J2067_007_volume_map (7).mrc using 72040 points
correlation = 0.5677, correlation about mean = 0.05338, overlap = 1387
steps = 156, shift = 2.11, angle = 5.74 degrees
Position of cryosparc_P8_J2925_004_volume_map (1).mrc (#3) relative to
cryosparc_P8_J2067_007_volume_map (7).mrc (#1) coordinates:
Matrix rotation and translation
-0.95369779 -0.30000030 0.02145559 379.30130107
-0.23140097 0.77744760 0.58483230 -73.94385412
-0.19213046 0.55278843 -0.81087042 228.42984382
Axis -0.14140594 0.94253082 0.30272101
Axis point 191.48557165 0.00000000 114.88444722
Rotation angle (degrees) 173.49415683
Shift along axis -54.17930559
> view matrix models
> #3,-0.99757,0.06955,0.0043675,318.34,0.069507,0.98855,0.13391,-93.862,0.0049958,0.13389,-0.99098,304.27
> fitmap #3 inMap #1
Fit map cryosparc_P8_J2925_004_volume_map (1).mrc in map
cryosparc_P8_J2067_007_volume_map (7).mrc using 72040 points
correlation = 0.9165, correlation about mean = 0.6178, overlap = 3640
steps = 104, shift = 2.6, angle = 8.19 degrees
Position of cryosparc_P8_J2925_004_volume_map (1).mrc (#3) relative to
cryosparc_P8_J2067_007_volume_map (7).mrc (#1) coordinates:
Matrix rotation and translation
-0.99745435 -0.07128823 0.00167430 347.71737025
-0.07066014 0.99127878 0.11123632 -60.86070385
-0.00958954 0.11083485 -0.99379257 312.67720271
Axis -0.03556501 0.99781730 0.05563965
Axis point 173.22061941 0.00000000 157.54651332
Rotation angle (degrees) 179.67660716
Shift along axis -55.69718209
> select clear
> volume #3 level 0.1082
> volume #1 level 0.1497
> volume #3 level 0.124
> volume #3 level 0.1366
> volume #3 level 0.1524
> show #!1 models
> select /T:28
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /T:29
33 atoms, 35 bonds, 1 residue, 1 model selected
> select add /T:28
65 atoms, 69 bonds, 2 residues, 1 model selected
> select add /T:30
98 atoms, 104 bonds, 3 residues, 1 model selected
> select add /T:31
130 atoms, 137 bonds, 4 residues, 1 model selected
> select add /T:33
163 atoms, 172 bonds, 5 residues, 1 model selected
> select add /T:32
193 atoms, 203 bonds, 6 residues, 1 model selected
> select add /T:34
225 atoms, 236 bonds, 7 residues, 1 model selected
> select add /T:35
257 atoms, 269 bonds, 8 residues, 1 model selected
> select add /T:36
289 atoms, 303 bonds, 9 residues, 3 models selected
> select clear
> select #1/T:26-39
Nothing selected
> select #2/T:26-39
444 atoms, 477 bonds, 14 residues, 1 model selected
> delete sel
> select /N:13
30 atoms, 31 bonds, 1 residue, 1 model selected
> select #2/N:1-13
408 atoms, 440 bonds, 13 residues, 1 model selected
> delete sel
> select /N:37
32 atoms, 33 bonds, 1 residue, 1 model selected
> select add /N:38
65 atoms, 67 bonds, 2 residues, 1 model selected
> select add /T:6
97 atoms, 100 bonds, 3 residues, 1 model selected
> select add /T:5
127 atoms, 131 bonds, 4 residues, 1 model selected
> select add /T:2
159 atoms, 165 bonds, 5 residues, 1 model selected
> select add /T:4
192 atoms, 200 bonds, 6 residues, 1 model selected
> select add /T:3
224 atoms, 234 bonds, 7 residues, 1 model selected
> delete sel
> select /T:9
32 atoms, 34 bonds, 1 residue, 1 model selected
> select up
601 atoms, 647 bonds, 19 residues, 1 model selected
> select up
63545 atoms, 64224 bonds, 3944 residues, 1 model selected
> select down
601 atoms, 647 bonds, 19 residues, 1 model selected
> select add /N:34
633 atoms, 681 bonds, 20 residues, 1 model selected
> select up
952 atoms, 1025 bonds, 30 residues, 1 model selected
> select add /Q:3
983 atoms, 1057 bonds, 31 residues, 1 model selected
> select up
1212 atoms, 1304 bonds, 38 residues, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
77 atoms, 82 bonds, 1 residue, 1 model selected
> select up
63545 atoms, 64224 bonds, 3944 residues, 1 model selected
> select down
77 atoms, 82 bonds, 1 residue, 1 model selected
> select add /Q:2
111 atoms, 118 bonds, 2 residues, 1 model selected
> select up
337 atoms, 361 bonds, 9 residues, 1 model selected
> select add /N:34
369 atoms, 395 bonds, 10 residues, 1 model selected
> select up
688 atoms, 739 bonds, 20 residues, 1 model selected
> select add /T:9
720 atoms, 773 bonds, 21 residues, 1 model selected
> select up
1289 atoms, 1386 bonds, 39 residues, 1 model selected
> select up
63545 atoms, 64224 bonds, 3944 residues, 1 model selected
> select down
1289 atoms, 1386 bonds, 39 residues, 1 model selected
> color zone #1 near sel distance 2.5
> volume #1 level 0.09521
> volume #1 level 0.1101
> undo
> close #2
> open
> /Users/janpetrovsky/Desktop/rnapol_p4a_isolda/final_model/isolda_phenix_7.pdb
Chain information for isolda_phenix_7.pdb #2
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
Q | No description available
T | No description available
> select add #2
64621 atoms, 65383 bonds, 31 pseudobonds, 3978 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> select ::name="B4P"
77 atoms, 82 bonds, 1 residue, 1 model selected
> show sel atoms
> select /Q:4
34 atoms, 36 bonds, 1 residue, 1 model selected
> select up
260 atoms, 279 bonds, 8 residues, 1 model selected
> color sel red
> select /T:7
30 atoms, 31 bonds, 1 residue, 1 model selected
> select up
1204 atoms, 1297 bonds, 38 residues, 1 model selected
> hide #!1 models
> color sel blue
> select /N:34
32 atoms, 34 bonds, 1 residue, 1 model selected
> select up
824 atoms, 887 bonds, 26 residues, 1 model selected
> color sel cyan
> select clear
> show #!1 models
> volume #1 level 0.09687
> select #2/N:1-13
408 atoms, 440 bonds, 13 residues, 1 model selected
> lsel
Unknown command: devel lsel
> delete sel
> select #2/T:28-39
384 atoms, 413 bonds, 12 residues, 1 model selected
> delete sel
> hide #!2 models
> show #!2 models
> hide #!1 models
> select /T:12
32 atoms, 34 bonds, 1 residue, 1 model selected
> select up
820 atoms, 883 bonds, 26 residues, 1 model selected
> select add /N:27
853 atoms, 918 bonds, 27 residues, 1 model selected
> select up
1236 atoms, 1330 bonds, 39 residues, 1 model selected
> select add /Q:8
1267 atoms, 1362 bonds, 40 residues, 1 model selected
> select up
1496 atoms, 1609 bonds, 47 residues, 1 model selected
> show #!1 models
> color zone #1 near sel distance 2.5
> color zone #1 near sel distance 3
> color zone #1 near sel distance 3.2
> color zone #1 near sel distance 3.5
> color zone #1 near sel distance 3.2
> volume #1 level 0.1051
> volume #1 level 0.1084
> color zone #1 near sel distance 3
> volume zone #1 nearAtoms sel range 3 newMap true
Opened cryosparc_P8_J2067_007_volume_map (7).mrc zone as #4, grid size
250,250,250, pixel 1.12, shown at step 1, values float32
> hide #!2 models
> volume #4 level 0.1194
> surface dust #4 size 11.2
> show #!2 models
> color zone #4 near sel distance 3
> hide #!2 models
> show #!1 models
> volume #1 level 0.1866
> color #1 #b2b2b23d models
> set bgColor white
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
> color #1 white models
> lighting soft
> lighting full
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting full
> color #1 #ebebebff models
> color #1 #ebebebce models
> color #1 white models
> color #1 #ffffff52 models
> show #!2 models
> graphics silhouettes false
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!3 models
> hide #!1 models
> lighting simple
> color #3 #ffffb270 models
> select #2/C
4076 atoms, 4118 bonds, 5 pseudobonds, 258 residues, 3 models selected
> select #2/Q
260 atoms, 279 bonds, 8 residues, 1 model selected
> view sel
> ui tool show "Side View"
> volume #3 level 0.1589
> volume #3 level 0.1557
> volume #3 level 0.1654
> volume #3 level 0.1492
> select /T:26
30 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> close #3
> lighting soft
> hide #!2 models
> show #!1 models
> show #!4 models
> lighting full
> lighting flat
> hide #!4 models
> show #!4 models
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> volume #1 level 0.1833
> volume #1 level 0.1569
> volume #4 level 0.117
> color #4 #b2ffffff models
> color zone #4 near sel distance 3
> show #!2 models
> select up
820 atoms, 883 bonds, 26 residues, 1 model selected
> select add /Q:2
854 atoms, 919 bonds, 27 residues, 1 model selected
> select up
1080 atoms, 1162 bonds, 34 residues, 1 model selected
> select add /N:36
1110 atoms, 1193 bonds, 35 residues, 1 model selected
> select up
1496 atoms, 1609 bonds, 47 residues, 1 model selected
> color zone #4 near sel distance 3
> hide #!2 models
> view name p1
> volume #1 level 0.1767
> select up
63829 atoms, 64529 bonds, 3953 residues, 1 model selected
> select down
1496 atoms, 1609 bonds, 47 residues, 1 model selected
> view name p1
> roll x 1 800
> roll y 1 360
> view name p2
> view name p3
> view name p4
> view name p5
> fly p1 p2 p3 p4 p5
> ui tool show "Side View"
> fly p1 p2 p3 p4 p5
> view name p4
> fly p1 p2 p3 p4 p5
> view name p2
> fly p1 p2 p3 p4 p5
> view name p4
> fly p1 p2 p3 p4 p5
> ui mousemode right pivot
> ui mousemode right "translate selected models"
> view name p1
> view name p2
> view name p3
> view name p4
> view name p5
> view name p6
> volume #4 level 0.1046
> fly p1 p2 p3 p4 p5 p6
> show #!2 models
> select ~sel & ##selected
62333 atoms, 62920 bonds, 30 pseudobonds, 3906 residues, 3 models selected
> hide sel cartoons
> volume #4 level 0.1013
> volume #4 level 0.1038
> hide #!4 models
> volume #1 level 0.1338
> volume #1 level 0.1024
> volume #1 level 0.18
> hide sel atoms
> select /Q:2
34 atoms, 36 bonds, 1 residue, 1 model selected
> select up
260 atoms, 279 bonds, 8 residues, 1 model selected
> select add /T:3
292 atoms, 313 bonds, 9 residues, 1 model selected
> select up
1080 atoms, 1162 bonds, 34 residues, 1 model selected
> hide sel cartoons
> roll y 1 360
> ui mousemode right pivot
> ui mousemode right "translate selected models"
> movie record
> roll y 1 360
> stop
> movie encode
Movie saved to /Users/janpetrovsky/Desktop/movie.mp4
> ui mousemode right pivot
> ui mousemode right "translate selected models"
> movie record
> roll y 1 360
> fly p1 p2 p3 p4 p5 p6
> stop
> encodew
Unknown command: movie encodew
> movie encode
Movie saved to /Users/janpetrovsky/Desktop/movie.mp4
> roll y 1 360
> movie record
> roll y 1 380
> roll x 1 90
> fly p1 p2 p3 p4 p5 p6
> stop
> movie encode
Movie saved to /Users/janpetrovsky/Desktop/movie.mp4
> view name p1
> fly p1 p2 p3 p4 p5 p6
> stop
> fly p1 p2 p3 p4 p5 p6
> stop
> movie record
> roll y 1 370
> select add #2
63829 atoms, 64529 bonds, 30 pseudobonds, 3953 residues, 3 models selected
> select subtract #2
Nothing selected
> select add #2
63829 atoms, 64529 bonds, 30 pseudobonds, 3953 residues, 3 models selected
> hide sel cartoons
> fly p20 p1 p2 p3 p4 p5 p6
fly: Unknown position name "p20"
> view name p20
> fly p20 p1 p2 p3 p4 p5 p6
> movie encode
Movie saved to /Users/janpetrovsky/Desktop/movie.mp4
> movie record
> roll y 1 370
> view name p20
> fly p20 p1 p2 p3 p4 p5 p6
> stop
> movie encode
Movie saved to /Users/janpetrovsky/Desktop/movie.mp4
> movie record
> roll y 1 370
> view name p20
> fly p20 p1 p2 p3 200 p4 p5 p6
> select up
63829 atoms, 64529 bonds, 30 pseudobonds, 3953 residues, 3 models selected
> select down
292 atoms, 313 bonds, 30 pseudobonds, 9 residues, 3 models selected
> movie encode
Movie saved to /Users/janpetrovsky/Desktop/movie.mp4
> view name p30
> lighting simple
> graphics silhouettes false
> hide #!4 models
> volume #1 color #ffffffb9
> volume #1 color #d6d6d6
> volume #1 level 0.1239
> volume #1 level 0.1074
> select ::name="B4P"
77 atoms, 82 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> volume #1 level 0.09911
> volume #4 level 0.08895
> hide #!2 models
> show #!2 models
> select add #2
63829 atoms, 64529 bonds, 30 pseudobonds, 3953 residues, 3 models selected
> show sel cartoons
> select clear
> select /Q:2
34 atoms, 36 bonds, 1 residue, 1 model selected
> select up
260 atoms, 279 bonds, 8 residues, 1 model selected
> select add /A:1@O3A
261 atoms, 279 bonds, 9 residues, 1 model selected
> select up
337 atoms, 361 bonds, 9 residues, 1 model selected
> select add /T:26
367 atoms, 392 bonds, 10 residues, 1 model selected
> select up
1157 atoms, 1244 bonds, 35 residues, 1 model selected
> select add /N:37
1189 atoms, 1277 bonds, 36 residues, 1 model selected
> select up
1573 atoms, 1691 bonds, 48 residues, 1 model selected
> color zone #4 near sel distance 3
> color zone #1 near sel distance 3
> select clear
> select /A:1@O2G
1 atom, 1 residue, 1 model selected
> select up
77 atoms, 82 bonds, 1 residue, 1 model selected
> color sel yellow
> color zone #1 near sel distance 3
> undo
> color sel byhetero
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
77 atoms, 82 bonds, 1 residue, 1 model selected
> color sel red
> select add /T:2
109 atoms, 116 bonds, 2 residues, 1 model selected
> select up
897 atoms, 965 bonds, 27 residues, 1 model selected
> select add /N:38
930 atoms, 999 bonds, 28 residues, 1 model selected
> select up
1313 atoms, 1412 bonds, 40 residues, 1 model selected
> color zone #1 near sel distance 3
> select add /Q:4
1347 atoms, 1448 bonds, 41 residues, 1 model selected
> select up
1573 atoms, 1691 bonds, 48 residues, 1 model selected
> color zone #1 near sel distance 3
> volume zone #1 nearAtoms sel range 3 newMap true
Opened cryosparc_P8_J2067_007_volume_map (7).mrc zone as #3, grid size
250,250,250, pixel 1.12, shown at step 1, values float32
> color zone #3 near sel distance 3
> surface dust #3 size 11.2
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> show #!4 models
> show #!1 models
> volume #1 level 0.1348
> volume #1 level 0.1314
> hide #!4 models
> show #!3 models
> p30
Unknown command: p30
> fly p30
> lighting flat
> volume #1 color #ffffff1d
> lighting full
> volume #1 color #ffffff1c
> lighting soft
> movie record
> roll y 1 370
> fly p20 p1 p2 p3 200 p4 p5 p6
> stop
> fly p30
> movie encode
Movie saved to /Users/janpetrovsky/Desktop/movie.mp4
> fly p30
> movie record
> roll y 1 370
> view name p20
> fly p20 p1 p2 p3 200 p4 p5 p6
> movie encode
Movie saved to /Users/janpetrovsky/Desktop/movie.mp4
> volume #1 color silver
> lighting simple
> transparency #3 80
> color #1 white models
> color #1 #ffffff3c models
> color #1 #ffffff3b models
> show #!2 models
> select ~sel & ##selected
62256 atoms, 62838 bonds, 30 pseudobonds, 3905 residues, 3 models selected
> hide sel cartoons
> select /T:27
30 atoms, 31 bonds, 1 residue, 1 model selected
> select up
820 atoms, 883 bonds, 26 residues, 1 model selected
> select /Q:2
34 atoms, 36 bonds, 1 residue, 1 model selected
> select up
260 atoms, 279 bonds, 8 residues, 1 model selected
> select /T:27
30 atoms, 31 bonds, 1 residue, 1 model selected
> select up
820 atoms, 883 bonds, 26 residues, 1 model selected
> select clear
> select #3
3 models selected
> select clear
> hide #!1 models
> select #3
3 models selected
> select clear
> hide #!3 models
> select /T:11
32 atoms, 33 bonds, 1 residue, 1 model selected
> select up
820 atoms, 883 bonds, 26 residues, 1 model selected
> select add /N:32
852 atoms, 916 bonds, 27 residues, 1 model selected
> select up
1236 atoms, 1330 bonds, 39 residues, 1 model selected
> select add /Q:2
1270 atoms, 1366 bonds, 40 residues, 1 model selected
> select up
1496 atoms, 1609 bonds, 47 residues, 1 model selected
> select add /A:1@N3B
1497 atoms, 1609 bonds, 48 residues, 1 model selected
> select up
1573 atoms, 1691 bonds, 48 residues, 1 model selected
> show #!3 models
> show #!1 models
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1496 atom styles
> color sel byhetero
> hide @h
> hide @H
> select @H
3705 atoms, 3705 residues, 1 model selected
> delete h
Missing or invalid "atoms" argument: invalid atoms specifier
> delete @h
> hide h
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide H
> transparency #3 90
> transparency #3 50
> transparency #3 40
> transparency #3 70
> view name 11
> cview sel
> select clear
> select #3
4 models selected
> hide #!3 models
> hide #!1 models
> select /A:1@N3A
1 atom, 1 residue, 1 model selected
> select up
77 atoms, 82 bonds, 1 residue, 1 model selected
> show #!3 models
> show #!1 models
> cview sel
> select /Q:2
34 atoms, 36 bonds, 1 residue, 1 model selected
> select up
260 atoms, 279 bonds, 8 residues, 1 model selected
> hide sel cartoons
> select /T:27
30 atoms, 31 bonds, 1 residue, 1 model selected
> select up
820 atoms, 883 bonds, 26 residues, 1 model selected
> hide sel cartoons
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 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 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac mini
Model Identifier: Mac14,3
Model Number: Z16L000FTCZ/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2 (23C64)
Kernel Version: Darwin 23.2.0
Time since boot: 101 days, 23 hours, 47 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
U27P2G6B:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
U2790B:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra 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-Clipper: 0.23.1
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-ISOLDE: 1.8
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 , 4 weeks 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 , 4 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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