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Opened 6 months ago
Closed 6 months ago
#17472 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: 1.9 (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 0x00000001f7f84f40 (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.pdb_lib._load_libs, 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, chimerax.surface._surface, 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, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 61)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,2",
"coalitionID" : 60361,
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"build" : "23G93",
"releaseType" : "User"
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"captureTime" : "2025-04-23 17:18:26.9760 -0700",
"codeSigningMonitor" : 1,
"incident" : "2657C987-3CBB-4107-8078-CECF69F5ED02",
"pid" : 8658,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-23 11:37:58.0841 -0700",
"procStartAbsTime" : 21796380979626,
"procExitAbsTime" : 22271818280791,
"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":"F5962B24-73D9-5811-802C-5EC5A9E388C3","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B7523C58-130A-FA01-2B0B-DC12327FC980",
"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" : 6180,
"sleepWakeUUID" : "8BAA2934-F8EE-49FA-A33C-3C7AB8E6DC14",
"sip" : "enabled",
"vmRegionInfo" : "0x44a625b7028 is not in any region. Bytes after previous region: 4236487913513 Bytes before following region: 100835592015832\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000044a625b7028","rawCodes":[1,4717524250664],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000044a625b7028"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":8658},
"vmregioninfo" : "0x44a625b7028 is not in any region. Bytes after previous region: 4236487913513 Bytes before following region: 100835592015832\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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===== 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/aleon/Desktop/ModelBuilding/3G11new/RealSpaceRefine_17/3G11_RS16-coot-0-combined_real_space_refined_017.pdb
Chain information for 3G11_RS16-coot-0-combined_real_space_refined_017.pdb #1
---
Chain | Description
A | No description available
B D F | No description available
C | No description available
E | No description available
H | No description available
L | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain /L
Alignment identifier is 1/L
> select /L:34
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /L:34
10 atoms, 9 bonds, 1 residue, 1 model selected
> close
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/3G11-reviewable/3G11_RS22_kabat.pdb"
Chain information for 3G11_RS22_kabat.pdb #1
---
Chain | Description
A | No description available
B D F | No description available
C | No description available
E | No description available
H | No description available
L | No description available
> close
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/6G8-reviewable/6G8_RSR_kabat_20.pdb"
Chain information for 6G8_RSR_kabat_20.pdb #1
---
Chain | Description
A C | No description available
B D F | No description available
E | No description available
H | No description available
L | No description available
> close
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/6H4-reviewable/6H4_RS56_kabat.pdb"
Chain information for 6H4_RS56_kabat.pdb #1
---
Chain | Description
A | No description available
B D F | No description available
C E | No description available
H | No description available
L | No description available
> close
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/5G01-reviewable/5G01_RS35_kabat.pdb"
Chain information for 5G01_RS35_kabat.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
H | No description available
L | No description available
> close
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/6H4-reviewable/6H4_RS56_kabat.pdb"
Chain information for 6H4_RS56_kabat.pdb #1
---
Chain | Description
A | No description available
B D F | No description available
C E | No description available
H | No description available
L | No description available
> close
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/6G8-reviewable/6G8_RSR_kabat_20.pdb"
Chain information for 6G8_RSR_kabat_20.pdb #1
---
Chain | Description
A C | No description available
B D F | No description available
E | No description available
H | No description available
L | No description available
> close
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/3G11-reviewable/3G11_RS22_kabat.pdb"
Chain information for 3G11_RS22_kabat.pdb #1
---
Chain | Description
A | No description available
B D F | No description available
C | No description available
E | No description available
H | No description available
L | No description available
> close
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/6H4-reviewable/6H4_RS56_kabat.pdb"
Chain information for 6H4_RS56_kabat.pdb #1
---
Chain | Description
A | No description available
B D F | No description available
C E | No description available
H | No description available
L | No description available
> ui tool show "Change Chain IDs"
> cloe
Unknown command: cloe
> close
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/6H4-reviewable/6H4_RS56_kabat.pdb"
Chain information for 6H4_RS56_kabat.pdb #1
---
Chain | Description
A | No description available
B D F | No description available
C E | No description available
H | No description available
L | No description available
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/3G11-reviewable/3G11_RS22_kabat.pdb"
Chain information for 3G11_RS22_kabat.pdb #2
---
Chain | Description
A | No description available
B D F | No description available
C | No description available
E | No description available
H | No description available
L | No description available
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/5G01-reviewable/5G01_RS35_kabat.pdb"
Chain information for 5G01_RS35_kabat.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
H | No description available
L | No description available
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/6G8-reviewable/6G8_RSR_kabat_20.pdb"
Chain information for 6G8_RSR_kabat_20.pdb #4
---
Chain | Description
A C | No description available
B D F | No description available
E | No description available
H | No description available
L | No description available
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide atoms
> show cartoons
> lighting soft
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 104644 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> mmaker #2/A to #1/A
Computing secondary structure
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 6H4_RS56_kabat.pdb, chain A (#1) with 3G11_RS22_kabat.pdb, chain A
(#2), sequence alignment score = 1462.7
RMSD between 318 pruned atom pairs is 0.740 angstroms; (across all 321 pairs:
0.766)
> mmaker #3/A to #1/A
Computing secondary structure
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 6H4_RS56_kabat.pdb, chain A (#1) with 5G01_RS35_kabat.pdb, chain A
(#3), sequence alignment score = 1481
RMSD between 310 pruned atom pairs is 0.875 angstroms; (across all 321 pairs:
0.962)
> mmaker #4/A to #1/A
Computing secondary structure
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 6H4_RS56_kabat.pdb, chain A (#1) with 6G8_RSR_kabat_20.pdb, chain A
(#4), sequence alignment score = 1471.9
RMSD between 323 pruned atom pairs is 0.679 angstroms; (across all 325 pairs:
0.701)
> select clear
Drag select of 2558 residues
> select up
51769 atoms, 52197 bonds, 3356 residues, 4 models selected
> select up
92023 atoms, 92988 bonds, 5935 residues, 4 models selected
> color sel light grey
> select clear
Drag select of 1122 residues, 3 pseudobonds
> select up
30560 atoms, 30808 bonds, 3 pseudobonds, 2021 residues, 7 models selected
> select up
61307 atoms, 61949 bonds, 3 pseudobonds, 3955 residues, 7 models selected
> color sel grey
> select clear
> save
> /Users/aleon/Desktop/ModelBuilding/FigureImages/FinalModelFigures/AllH15ModelsAligned.cxs
> includeMaps true
> open
> /Users/aleon/Desktop/ModelBuilding/6F6new/6F6_with6G8H15_chainRefined_newStart.pdb
Chain information for 6F6_with6G8H15_chainRefined_newStart.pdb #5
---
Chain | Description
A C E | No description available
B D F | No description available
H | No description available
L | No description available
> hide atoms
> show cartoons
> mmaker #5/E to #1/A
Computing secondary structure
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 6H4_RS56_kabat.pdb, chain A (#1) with
6F6_with6G8H15_chainRefined_newStart.pdb, chain E (#5), sequence alignment
score = 1412.5
RMSD between 324 pruned atom pairs is 0.697 angstroms; (across all 325 pairs:
0.706)
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 13443 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
Drag select of 1014 residues
> select up
8766 atoms, 8901 bonds, 1118 residues, 1 model selected
> select up
11661 atoms, 11882 bonds, 1488 residues, 1 model selected
> color sel grey
> select clear
> select #5/F:445
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/E:82
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #5/F:438
14 atoms, 13 bonds, 2 residues, 1 model selected
> select up
493 atoms, 499 bonds, 59 residues, 1 model selected
> select up
3887 atoms, 3959 bonds, 496 residues, 1 model selected
> color sel light grey
> select clear
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!4 models
> hide #5 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> save
> /Users/aleon/Desktop/ModelBuilding/FigureImages/FinalModelFigures/AllH15ModelsAligned.cxs
> includeMaps true
> hide #!2 models
> show #!2 models
> hide #!4 models
Drag select of 745 residues, 2 pseudobonds
> select up
14131 atoms, 14237 bonds, 2 pseudobonds, 908 residues, 2 models selected
> select up
22691 atoms, 22928 bonds, 2 pseudobonds, 1463 residues, 2 models selected
> hide sel
> hide sel cartoons
> show #!4 models
> select clear
Drag select of 616 residues, 2 pseudobonds
> select up
13410 atoms, 13519 bonds, 2 pseudobonds, 859 residues, 2 models selected
> select up
23259 atoms, 23505 bonds, 2 pseudobonds, 1499 residues, 2 models selected
> show sel surfaces
> hide sel cartoons
> select clear
> color #BB3C19 #2/H
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #2/H
1776 atoms, 1801 bonds, 119 residues, 1 model selected
> color sel #BB3C19
> select #2/L
1680 atoms, 1705 bonds, 111 residues, 1 model selected
> color sel #FF7F50
> select #3/H
1856 atoms, 1876 bonds, 123 residues, 1 model selected
> select #4/H
1782 atoms, 1806 bonds, 119 residues, 1 model selected
> color sel #C13C5F
> select #4/L
1678 atoms, 1700 bonds, 111 residues, 1 model selected
> color sel #D16783
> select clear
> set bgColor white
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> select #1/H
1694 atoms, 1717 bonds, 115 residues, 1 model selected
> color sel #558E72
> color sel #98C6B0
> select #1/H
1694 atoms, 1717 bonds, 115 residues, 1 model selected
> color sel #558E72
> select #1/L
1732 atoms, 1756 bonds, 113 residues, 1 model selected
> color sel #98C6B0
> select clear
> hide #!1 models
> hide #!4 models
> show #!4 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> select #3/H
1856 atoms, 1876 bonds, 123 residues, 1 model selected
> color sel #DAD432
> select #3/L
1636 atoms, 1658 bonds, 108 residues, 1 model selected
> color sel #FFFB81
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> select #2/H
1776 atoms, 1801 bonds, 119 residues, 1 model selected
> color sel #2D609F
> select #2/L
1680 atoms, 1705 bonds, 111 residues, 1 model selected
> color sel #74A8E7
> select clear
> save
> /Users/aleon/Desktop/ModelBuilding/FigureImages/FinalModelFigures/3G11_6G8_Overlay.cxs
> includeMaps true
> ui tool show "Side View"
Drag select of 167 residues
> select up
4737 atoms, 4791 bonds, 309 residues, 2 models selected
> select up
6916 atoms, 7012 bonds, 460 residues, 2 models selected
> hide sel cartoons
> select #2/H:29-35,51-47,100A-95
124 atoms, 128 bonds, 7 residues, 1 model selected
> show sel cartoons
> select #2/H:29-35,47-51,95-100A
304 atoms, 311 bonds, 19 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #2/H:29-35,51-57,95-100A
333 atoms, 340 bonds, 22 residues, 1 model selected
> show sel cartoons
> select #2/H:25-35,51-57,95-100A
383 atoms, 391 bonds, 26 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #2/H:28-35,51-57,95-100A
344 atoms, 351 bonds, 23 residues, 1 model selected
> show sel cartoons
> select clear
> select #4/H:28-35,51-57,95-100A
352 atoms, 359 bonds, 23 residues, 1 model selected
> show sel cartoons
> select clear
> select #4/L:27C-31,90-95
179 atoms, 181 bonds, 12 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #4/L:27C-31,91-95
162 atoms, 164 bonds, 11 residues, 1 model selected
> show sel cartoons
> select #2/L:27C-31,91-95
161 atoms, 163 bonds, 11 residues, 1 model selected
> show sel cartoons
> select clear
> lighting soft
> graphics silhouettes true
> lighting gentle
> lighting soft
> select #4/E:207@CA
1 atom, 1 residue, 1 model selected
> select add #4/C:207@N
2 atoms, 2 residues, 2 models selected
> select up
14 atoms, 12 bonds, 2 residues, 3 models selected
> select up
166 atoms, 164 bonds, 12 residues, 3 models selected
> select up
10041 atoms, 10150 bonds, 657 residues, 3 models selected
> hide sel surfaces
> select #4/F:423@CD
1 atom, 1 residue, 1 model selected
> select add #4/D:414@C
2 atoms, 2 residues, 2 models selected
> select down
2 atoms, 2 residues, 3 models selected
> select up
34 atoms, 32 bonds, 2 residues, 3 models selected
> select up
634 atoms, 636 bonds, 38 residues, 3 models selected
> hide sel surfaces
> select #4/F:429@CG2
1 atom, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 1 residue, 2 models selected
> select up
837 atoms, 843 bonds, 51 residues, 2 models selected
> select up
2747 atoms, 2774 bonds, 172 residues, 2 models selected
> hide sel surfaces
> select #4/D:404@O
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 2 models selected
> select up
291 atoms, 291 bonds, 18 residues, 2 models selected
> select up
2747 atoms, 2774 bonds, 172 residues, 2 models selected
> hide sel surfaces
> graphics silhouettes false
> graphics silhouettes true
> show #!3 models
> hide #!3 models
> save 6G8_classCDRs.png supersample 8 transparentBackground true
> select #2/H:35
17 atoms, 17 bonds, 1 residue, 1 model selected
> select add #4/H:35
34 atoms, 34 bonds, 2 residues, 2 models selected
> hide sel cartoons
> select #2/H:28
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #4/H:28
22 atoms, 20 bonds, 2 residues, 2 models selected
> hide sel cartoons
> select #2/H:29
20 atoms, 20 bonds, 1 residue, 1 model selected
> select add #4/H:29
40 atoms, 40 bonds, 2 residues, 2 models selected
> hide sel cartoons
> save 6G8_classCDRs.png supersample 8 transparentBackground true
> hide #!2 models
> select #4/A
5002 atoms, 5056 bonds, 1 pseudobond, 327 residues, 2 models selected
> hide sel surfaces
> select #4/B:423@OE2
1 atom, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 1 residue, 2 models selected
> select up
298 atoms, 299 bonds, 18 residues, 2 models selected
> select up
2722 atoms, 2748 bonds, 171 residues, 2 models selected
> hide sel surfaces
> select #4/A
5002 atoms, 5056 bonds, 1 pseudobond, 327 residues, 2 models selected
> show sel cartoons
> select clear
> select #4/A:166,167,168,169,206
75 atoms, 73 bonds, 5 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #4/H:33,56,52,99,100,97
106 atoms, 106 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> save
> /Users/aleon/Desktop/ModelBuilding/FigureImages/FinalModelFigures/6G8_Class_HC_interactions.cxs
> includeMaps true
> select #4/H:33,56,52,99,100,97
106 atoms, 106 bonds, 6 residues, 1 model selected
> ui tool show H-Bonds
> select #4/H:33,56,52,99,100,97
106 atoms, 106 bonds, 6 residues, 1 model selected
> select #4/A:166,167,168,169,206
75 atoms, 73 bonds, 5 residues, 1 model selected
> select #4/H:33,56,52,99,100,97
106 atoms, 106 bonds, 6 residues, 1 model selected
> /A:166,167,168,169,206
Unknown command: /A:166,167,168,169,206
> select #4/H:33,56,52,99,100,97,#4/A:166,167,168,169,206
Expected an objects specifier or a keyword
> select #4/H:33,56,52,99,100,97
106 atoms, 106 bonds, 6 residues, 1 model selected
> select H
51933 atoms, 6855 residues, 4 models selected
> hide sel & #!4 atoms
> select #4/H:33,56,52,99,100,97
106 atoms, 106 bonds, 6 residues, 1 model selected
> hbonds sel color #000000 interModel false intraMol false intraRes false
> reveal true
3 hydrogen bonds found
> ui tool show H-Bonds
> hbonds delete
> select H
51933 atoms, 6855 residues, 4 models selected
> hide sel & #!4 atoms
> select clear
> select #4/L
1678 atoms, 1700 bonds, 111 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select clear
> select #4/A:206
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add #4/H:97@CD1
15 atoms, 13 bonds, 2 residues, 2 models selected
> select #4/H:97@CD1
1 atom, 1 residue, 1 model selected
> select clear
> select add #4/A:206
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add #4/H:97
35 atoms, 34 bonds, 2 residues, 2 models selected
> hbonds sel color #424242 restrict both interModel false intraMol false
> intraRes false reveal true
0 hydrogen bonds found
> show sel atoms
> hbonds sel color #424242 restrict both interModel false intraMol false
> intraRes false reveal true
0 hydrogen bonds found
> hbonds sel color #424242 restrict both interModel false distSlop 0.5
> intraMol false intraRes false reveal true
0 hydrogen bonds found
> hbonds sel color #424242 restrict both interModel false distSlop 0.6
> intraMol false intraRes false reveal true
0 hydrogen bonds found
> hbonds sel color #424242 restrict both interModel false distSlop 0.8
> intraMol false intraRes false reveal true
0 hydrogen bonds found
> hbonds sel color #424242 restrict both interModel false angleSlop 30.0
> intraMol false intraRes false reveal true
0 hydrogen bonds found
> hbonds sel color #424242 interModel false angleSlop 30.0 intraMol false
> intraRes false reveal true
0 hydrogen bonds found
> hbonds sel color #424242 interModel false angleSlop 50.0 intraMol false
> intraRes false reveal true
1 hydrogen bonds found
> select clear
> select #4/H:97
21 atoms, 21 bonds, 1 residue, 1 model selected
> hbonds sel color #797979 interModel false angleSlop 50.0 intraMol false
> intraRes false reveal true
1 hydrogen bonds found
> hbonds sel color #919191 interModel false angleSlop 50.0 intraMol false
> intraRes false reveal true
1 hydrogen bonds found
> select clear
> select #4/H:33,56,52,99,100,97 again
Expected a keyword
> select #4/H:33,56,52,99,100,97
106 atoms, 106 bonds, 6 residues, 1 model selected
> hbonds sel color #919191 interModel false angleSlop 50.0 intraMol false
> intraRes false reveal true
5 hydrogen bonds found
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> hbonds sel color #797979 interModel false angleSlop 50.0 intraMol false
> intraRes false reveal true
1 hydrogen bonds found
> hide sel atoms
> select #4/H:33,56,52,99,100,97
106 atoms, 106 bonds, 6 residues, 1 model selected
> hbonds sel color #797979 interModel false angleSlop 50.0 intraMol false
> intraRes false reveal true
5 hydrogen bonds found
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select H
51933 atoms, 6855 residues, 4 models selected
> hide sel & #!4 atoms
===== 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 - 88.1
OpenGL renderer: Apple M1 Max
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 Pro
Model Identifier: MacBookPro18,2
Model Number: Z14W00106LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 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: 22 days, 19 hours, 42 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 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
babel: 2.16.0
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-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-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
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
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
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
packaging: 23.2
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
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
tornado: 6.4.2
traitlets: 5.14.3
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-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 6 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 , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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