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Opened 7 weeks ago
Closed 7 weeks ago
#18683 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6.1-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 0x000000020cac20c0 (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, chimerax.surface._surface, 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.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, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 61)
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"procRole" : "Background",
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"incident" : "4401130E-8DBE-4F36-A088-DA35A6B65522",
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"procLaunch" : "2025-09-01 15:02:10.4877 +0200",
"procStartAbsTime" : 3202001703169,
"procExitAbsTime" : 4371095209787,
"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"},
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "41EB562E-A196-C0AA-1FF8-4D81EBE3412B",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
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"wakeTime" : 1554,
"sleepWakeUUID" : "5598F7E3-C95A-411A-9C13-EA4F6EF60DB5",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4373413527\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104ad0000-104ad4000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":14995},
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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/anushkaghosh/Downloads/HTHP_bessy200319_C2221.pdb
Chain information for HTHP_bessy200319_C2221.pdb #1
---
Chain | Description
A B E | No description available
C D F | No description available
64 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> set bgColor white
> show cartoons
Computing secondary structure
> style stick
Changed 7585 atom styles
> hide atoms
> ui tool show "Crystal Contacts"
> crystalcontacts #1 distance 1
1 pairs of asymmetric units of HTHP_bessy200319_C2221.pdb contact at distance
1.0 A
Atoms MTRIX SMTRY Unit cell MTRIXref Copies
2 0 2 0 0 -1 0 1
> crystalcontacts delete #1
> crystalcontacts #1 distance 1 rainbow false
1 pairs of asymmetric units of HTHP_bessy200319_C2221.pdb contact at distance
1.0 A
Atoms MTRIX SMTRY Unit cell MTRIXref Copies
2 0 2 0 0 -1 0 1
> open
> /Users/anushkaghosh/Documents/Documents/Xtal/DTHP_K40TQ47K_refine_026-coot-0.pdb
Chain information for DTHP_K40TQ47K_refine_026-coot-0.pdb #3
---
Chain | Description
A | No description available
B E | No description available
C | No description available
D F | No description available
64 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!2 models
> hide #!1 models
> select add #3
7599 atoms, 7554 bonds, 33 pseudobonds, 577 residues, 3 models selected
> show sel cartoons
Computing secondary structure
> style sel stick
Changed 7599 atom styles
> hide sel atoms
> show #!1 models
> select add #1
15184 atoms, 14994 bonds, 57 pseudobonds, 1253 residues, 5 models selected
> ui tool show Matchmaker
> matchmaker #!3 to #1
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 HTHP_bessy200319_C2221.pdb, chain B (#1) with
DTHP_K40TQ47K_refine_026-coot-0.pdb, chain B (#3), sequence alignment score =
367.7
RMSD between 73 pruned atom pairs is 0.251 angstroms; (across all 73 pairs:
0.251)
> hide #!1 models
> select subtract #1
7599 atoms, 7554 bonds, 33 pseudobonds, 577 residues, 3 models selected
> crystalcontacts #3 distance 1 rainbow false
1 pairs of asymmetric units of DTHP_K40TQ47K_refine_026-coot-0.pdb contact at
distance 1.0 A
Atoms MTRIX SMTRY Unit cell MTRIXref Copies
1 0 1 0 0 0 0 1
> show #!2 models
> show #!1 models
> hide #!4 models
> hide #!2 models
> open
> /Users/anushkaghosh/Documents/Documents/Xtal/HTHP_T38KK45Q_refine_014-coot-0.pdb
Chain information for HTHP_T38KK45Q_refine_014-coot-0.pdb #5
---
Chain | Description
A E | No description available
B | No description available
C D F | No description available
64 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!3 models
> hide #!1 models
> select subtract #3
Nothing selected
> select add #5
7442 atoms, 7469 bonds, 30 pseudobonds, 506 residues, 2 models selected
> show sel cartoons
Computing secondary structure
> style sel stick
Changed 7442 atom styles
> hide sel atoms
> show #!1 models
> show #!3 models
> crystalcontacts #5 distance 1 rainbow false
0 pairs of asymmetric units of HTHP_T38KK45Q_refine_014-coot-0.pdb contact at
distance 1.0 A
> crystalcontacts #5 distance 2 rainbow false
6 pairs of asymmetric units of HTHP_T38KK45Q_refine_014-coot-0.pdb contact at
distance 2.0 A
Atoms MTRIX SMTRY Unit cell MTRIXref Copies
5 0 2 0 0 -1 0 1
2 0 7 0 0 0 0 1
2 0 7 -1 0 0 0 1
2 0 6 0 0 -1 0 1
2 0 6 0 -1 -1 0 1
1 0 2 1 0 -1 0 1
> show #!2 models
> hide #!3 models
> hide #!6 models
> hide #!1 models
> hide #!2 models
> hide #!5 models
> matchmaker #!5 to #1
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 HTHP_bessy200319_C2221.pdb, chain C (#1) with
HTHP_T38KK45Q_refine_014-coot-0.pdb, chain B (#5), sequence alignment score =
374
RMSD between 74 pruned atom pairs is 0.494 angstroms; (across all 74 pairs:
0.494)
> show #!3 models
> show #!5 models
> select subtract #5
Nothing selected
> show #!1 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!6 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> crystalcontacts delete #5
> crystalcontacts #5 distance 1 rainbow false
0 pairs of asymmetric units of HTHP_T38KK45Q_refine_014-coot-0.pdb contact at
distance 1.0 A
> crystalcontacts #5 distance 2 rainbow false
6 pairs of asymmetric units of HTHP_T38KK45Q_refine_014-coot-0.pdb contact at
distance 2.0 A
Atoms MTRIX SMTRY Unit cell MTRIXref Copies
5 0 2 0 0 -1 0 1
2 0 7 0 0 0 0 1
2 0 7 -1 0 0 0 1
2 0 6 0 0 -1 0 1
2 0 6 0 -1 -1 0 1
1 0 2 1 0 -1 0 1
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!6 models
> hide #!5 models
> hide #!3 models
> show #!2 models
> select #1/D:40
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2.1/B:40
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #1/D:43
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/D:46
15 atoms, 14 bonds, 1 residue, 1 model selected
> select clear
> select #1/D:47
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2.1/B:47
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/A
1220 atoms, 1233 bonds, 4 pseudobonds, 75 residues, 2 models selected
> select #1/A#2.1/A#3/A#4.1/A#5/A#6.1/A#6.2/A#6.3/A#6.4/A#6.5/A#6.6/A
13417 atoms, 13565 bonds, 55 pseudobonds, 818 residues, 24 models selected
> select #1/A:47
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:40
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1-6/A:40
226 atoms, 215 bonds, 11 residues, 11 models selected
> show sel & #!1#!2.1 atoms
> select #1-6/A:47
197 atoms, 186 bonds, 11 residues, 11 models selected
> show sel & #!1#!2.1 atoms
> select clear
> color #1-2 red
> undo
> select #1-6/A:47
197 atoms, 186 bonds, 11 residues, 11 models selected
> color (#!1#!2.1 & sel) red
> select #1-6/A:40
226 atoms, 215 bonds, 11 residues, 11 models selected
> color (#!1#!2.1 & sel) blue
> select #1-6/A-F:40
1356 atoms, 1290 bonds, 66 residues, 11 models selected
> show sel & #!1#!2.1 atoms
> color (#!1#!2.1 & sel) blue
> select #1-6/A-F:47
1182 atoms, 1116 bonds, 66 residues, 11 models selected
> color (#!1#!2.1 & sel) red
> show sel & #!1#!2.1 atoms
> select #1-6/A-F:47
1182 atoms, 1116 bonds, 66 residues, 11 models selected
> show hbonds
> select #1-6/A-F:40
1356 atoms, 1290 bonds, 66 residues, 11 models selected
> show hbonds
> select clear
> select #2.1/E:47@NE2
1 atom, 1 residue, 1 model selected
> select #1/F:54
10 atoms, 9 bonds, 1 residue, 1 model selected
> select clear
> select #2.1/E:47
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> show #!3 models
> hide #!2 models
> hide #!1 models
> select #1-6/A-F:40
1356 atoms, 1290 bonds, 66 residues, 11 models selected
> show sel & #!3 atoms
> color (#!3 & sel) gray
> color (#!3 & sel) black
> select #1-6/A-F:47
1182 atoms, 1116 bonds, 66 residues, 11 models selected
> color (#!3 & sel) black
> show sel & #!3 atoms
> show #!1 models
> select clear
> show #!2 models
> show #!4 models
> hide #!2 models
> hide #!1 models
> select #1-6/A-F:47
1182 atoms, 1116 bonds, 66 residues, 11 models selected
> show (#!3#!4.1 & sel) target ab
> select #1-6/A-F:40
1356 atoms, 1290 bonds, 66 residues, 11 models selected
> show sel & #!3#!4.1 atoms
> select clear
> ui tool show "Side View"
> view
> 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
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> 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
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting simple
> lighting soft
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> set bgColor white
> 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
> select ::name="HEM"
4818 atoms, 5016 bonds, 264 pseudobonds, 66 residues, 22 models selected
> show sel & #!3#!4.1 atoms
> select clear
> select ::name="HEM"
4818 atoms, 5016 bonds, 264 pseudobonds, 66 residues, 22 models selected
> color (#!3#!4.1 & sel) dark gray
> select Fe
66 atoms, 66 residues, 11 models selected
> style (#!3#!4.1 & sel) sphere
Changed 12 atom styles
> color (#!3#!4.1 & sel) black
> select clear
> select #1-6/A-F
81362 atoms, 82239 bonds, 324 pseudobonds, 4980 residues, 24 models selected
> color (#!3#!4.1 & sel) #b4aaffff
> undo
> select #1-6/A-F:40
1356 atoms, 1290 bonds, 66 residues, 11 models selected
> select #1-6/A-F
81362 atoms, 82239 bonds, 324 pseudobonds, 4980 residues, 24 models selected
> color (#!3#!4.1 & sel) #ffaf3dff
> color (#!3#!4.1 & sel) #b4aaffff
> color (#!3#!4.1 & sel) #b4aafffc
> color (#!3#!4.1 & sel) #b4aaffda
> color (#!3#!4.1 & sel) #b4aaffd0
> color (#!3#!4.1 & sel) #b4aaffd1
> color (#!3#!4.1 & sel) #b4aaffe4
> color (#!3#!4.1 & sel) #b4aaffe7
> color (#!3#!4.1 & sel) #b4aafff0
> color (#!3#!4.1 & sel) #b4aafff1
> color (#!3#!4.1 & sel) #b4aaffff
> color (#!3#!4.1 & sel) #b4aaff19
> color (#!3#!4.1 & sel) #b4aaff1b
> color (#!3#!4.1 & sel) #b4aaffde
> color (#!3#!4.1 & sel) #b4aaffff
> color (#!3#!4.1 & sel) #b1aeffff
> color (#!3#!4.1 & sel) #b3b0ffff
> color (#!3#!4.1 & sel) #b5b4ffff
> color (#!3#!4.1 & sel) #b5b5ffff
> color (#!3#!4.1 & sel) #b7b6ffff
> color (#!3#!4.1 & sel) #bab9ffff
> color (#!3#!4.1 & sel) #c0bdffff
> color (#!3#!4.1 & sel) #c0beffff
> color (#!3#!4.1 & sel) #c2bfffff
> color (#!3#!4.1 & sel) #b4aaffff
> select ::name="HEM"
4818 atoms, 5016 bonds, 264 pseudobonds, 66 residues, 22 models selected
> color (#!3#!4.1 & sel) dark gray
> select Fe
66 atoms, 66 residues, 11 models selected
> color (#!3#!4.1 & sel) black
> select clear
> select ::name="HEM"
4818 atoms, 5016 bonds, 264 pseudobonds, 66 residues, 22 models selected
> color (#!3#!4.1 & sel) #4fb43fff
> color (#!3#!4.1 & sel) #ffaf3dff
> color (#!3#!4.1 & sel) #fb72f9ff
> color (#!3#!4.1 & sel) #fb80f8ff
> color (#!3#!4.1 & sel) #fb88f6ff
> color (#!3#!4.1 & sel) #fb8df4ff
> color (#!3#!4.1 & sel) #fbbdfbff
> color (#!3#!4.1 & sel) #f6cefbff
> color (#!3#!4.1 & sel) #f4d6fbff
> color (#!3#!4.1 & sel) #fbe6f5ff
> color (#!3#!4.1 & sel) #fbe7efff
> color (#!3#!4.1 & sel) #fbe6eaff
> color (#!3#!4.1 & sel) #fbe6e8ff
> color (#!3#!4.1 & sel) #fbe6e6ff
> color (#!3#!4.1 & sel) #fbe9e4ff
> color (#!3#!4.1 & sel) #fbe0e5ff
> color (#!3#!4.1 & sel) #e1e1e1ff
> color (#!3#!4.1 & sel) #b8b8b8ff
> color (#!3#!4.1 & sel) #a2a2a2ff
> color (#!3#!4.1 & sel) #8c8c8cff
> color (#!3#!4.1 & sel) #8f8f8fff
> color (#!3#!4.1 & sel) #a9a9a9ff
> color (#!3#!4.1 & sel) #afafafff
> color (#!3#!4.1 & sel) #b5b5b5ff
> color (#!3#!4.1 & sel) #bababaff
> color (#!3#!4.1 & sel) #929292ff
> color (#!3#!4.1 & sel) #707070ff
> color (#!3#!4.1 & sel) #595959ff
> color (#!3#!4.1 & sel) #414141ff
> color (#!3#!4.1 & sel) #2b2b2bff
> color (#!3#!4.1 & sel) #222222ff
> color (#!3#!4.1 & sel) #212121ff
> color (#!3#!4.1 & sel) #2f2f2fff
> color (#!3#!4.1 & sel) #404040ff
> color (#!3#!4.1 & sel) #454545ff
> color (#!3#!4.1 & sel) #494949ff
> color (#!3#!4.1 & sel) #505050ff
> color (#!3#!4.1 & sel) #515151ff
> color (#!3#!4.1 & sel) #585858ff
> color (#!3#!4.1 & sel) #5b5b5bff
> color (#!3#!4.1 & sel) #606060ff
> color (#!3#!4.1 & sel) #626262ff
> color (#!3#!4.1 & sel) #8d8d8dff
> color (#!3#!4.1 & sel) #afafafff
> color (#!3#!4.1 & sel) #bababaff
> color (#!3#!4.1 & sel) #bcbcbcff
> color (#!3#!4.1 & sel) #bdbdbdff
> color (#!3#!4.1 & sel) #c9c9c9ff
> color (#!3#!4.1 & sel) #cbcbcbff
> color (#!3#!4.1 & sel) #cececeff
> color (#!3#!4.1 & sel) #cdcdcdff
> color (#!3#!4.1 & sel) #cbcbcbff
> color (#!3#!4.1 & sel) #c8c8c8ff
> color (#!3#!4.1 & sel) #c7c7c7ff
> color (#!3#!4.1 & sel) #929292ff
> color (#!3#!4.1 & sel) #a9a9a9ff
> color (#!3#!4.1 & sel) #c0c0c0ff
> color (#!3#!4.1 & sel) #d6d6d6ff
> color (#!3#!4.1 & sel) #ebebebff
> color (#!3#!4.1 & sel) #d6d6d6ff
> color (#!3#!4.1 & sel) #c0c0c0ff
> color (#!3#!4.1 & sel) #ffffffff
> color (#!3#!4.1 & sel) #c0c0c0ff
> color (#!3#!4.1 & sel) #d6d6d6ff
> select Fe
66 atoms, 66 residues, 11 models selected
> color (#!3#!4.1 & sel) #5e5e5eff
> color (#!3#!4.1 & sel) #424242ff
> color (#!3#!4.1 & sel) #212121ff
> select clear
> select #1-6/A-F:40
1356 atoms, 1290 bonds, 66 residues, 11 models selected
> color (#!3#!4.1 & sel) purple
> color (#!3#!4.1 & sel) #ff40ffff
> color (#!3#!4.1 & sel) #ff85ffff
> color (#!3#!4.1 & sel) #ff8ad8ff
> color (#!3#!4.1 & sel) #ff2f92ff
> color (#!3#!4.1 & sel) #fffb00ff
> color (#!3#!4.1 & sel) #fffc79ff
> color (#!3#!4.1 & sel) #ffd479ff
> color (#!3#!4.1 & sel) #ffe178ff
> color (#!3#!4.1 & sel) #ffe96aff
> color (#!3#!4.1 & sel) #ffeb68ff
> color (#!3#!4.1 & sel) #ffeb67ff
> color (#!3#!4.1 & sel) #ffed63ff
> color (#!3#!4.1 & sel) #ffed62ff
> color (#!3#!4.1 & sel) #ffee61ff
> color (#!3#!4.1 & sel) #ffef5fff
> color (#!3#!4.1 & sel) #fff05eff
> color (#!3#!4.1 & sel) #fff05fff
> color (#!3#!4.1 & sel) #ffe667ff
> color (#!3#!4.1 & sel) #ffe36aff
> color (#!3#!4.1 & sel) #ffe26aff
> color (#!3#!4.1 & sel) #ffdd6fff
> color (#!3#!4.1 & sel) #ffdc70ff
> color (#!3#!4.1 & sel) #ffdb70ff
> color (#!3#!4.1 & sel) #ffd971ff
> color (#!3#!4.1 & sel) #ffd870ff
> color (#!3#!4.1 & sel) #ffd76eff
> color (#!3#!4.1 & sel) #ffd76cff
> color (#!3#!4.1 & sel) #ffd66bff
> color (#!3#!4.1 & sel) #ffd267ff
> color (#!3#!4.1 & sel) #ffcf64ff
> color (#!3#!4.1 & sel) #ffcf63ff
> color (#!3#!4.1 & sel) #ffd064ff
> color (#!3#!4.1 & sel) #ffd065ff
> color (#!3#!4.1 & sel) #ffd165ff
> color (#!3#!4.1 & sel) #ffd166ff
> color (#!3#!4.1 & sel) #deb658ff
> color (#!3#!4.1 & sel) #c9a550ff
> color (#!3#!4.1 & sel) #bf9d4cff
> color (#!3#!4.1 & sel) #a88a43ff
> color (#!3#!4.1 & sel) #9b7f3eff
> color (#!3#!4.1 & sel) #ad8e45ff
> color (#!3#!4.1 & sel) #b9984aff
> color (#!3#!4.1 & sel) #e5bc5bff
> color (#!3#!4.1 & sel) #e9bf5dff
> color (#!3#!4.1 & sel) #eac05dff
> color (#!3#!4.1 & sel) #eec45fff
> color (#!3#!4.1 & sel) #f4c961ff
> color (#!3#!4.1 & sel) #f5c962ff
> color (#!3#!4.1 & sel) #ffd166ff
> color (#!3#!4.1 & sel) #ffe35eff
> color (#!3#!4.1 & sel) #ffed54ff
> color (#!3#!4.1 & sel) #ffea5aff
> color (#!3#!4.1 & sel) #ffe75dff
> color (#!3#!4.1 & sel) #ffe65fff
> color (#!3#!4.1 & sel) #ffe461ff
> color (#!3#!4.1 & sel) #ffe364ff
> color (#!3#!4.1 & sel) #ffe167ff
> color (#!3#!4.1 & sel) #ffda71ff
> color (#!3#!4.1 & sel) #ffd872ff
> color (#!3#!4.1 & sel) #ffd572ff
> color (#!3#!4.1 & sel) #ffd479ff
> select clear
> select #1-6/A-F:47
1182 atoms, 1116 bonds, 66 residues, 11 models selected
> color (#!3#!4.1 & sel) #ffd479ff
> select clear
> hide H
> save
> /Users/anushkaghosh/Documents/Documents/chimaera/DTHP_double_mutants/Q47KK40T-full.png
> width 1329 height 782 supersample 3 transparentBackground true
> view
> select #1-6/A-F:40,47
2538 atoms, 2406 bonds, 132 residues, 11 models selected
> view sel
> hide #* target a
> show (#!3#!4.1 & sel) target ab
> label (#!3#!4.1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> hide H
> select clear
> select #4.1/B:47@NZ
1 atom, 1 residue, 1 model selected
> select add #3/A:40@OG1
2 atoms, 2 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #ff202d restrict cross interModel false intraModel false
> intraMol false intraRes false reveal true
0 hydrogen bonds found
> hbonds sel color #ff202d restrict cross interModel false intraModel false
> intraMol false intraRes false reveal true
0 hydrogen bonds found
> hbonds sel color #ff202d restrict cross reveal true
2 hydrogen bonds found
> show hbonds
> ui tool show "Check Waters"
> hbonds #3/S:2-674 interModel false reveal true restrict any name "water
> H-bonds"
332 hydrogen bonds found
> select #3/S:2-674
119 atoms, 178 pseudobonds, 119 residues, 2 models selected
> display #3/S:2-674 : view #3/S:2-674 @ hide hbonds
No waters chosen
> delete
Missing or invalid "atoms" argument: empty atom specifier
> hide
> select #1-6/A-F:40,47
2538 atoms, 2406 bonds, 132 residues, 11 models selected
> show sel & #!3#!4.1 atoms
> hide
> show sel & #!3#!4.1 atoms
> hide H
> select clear
> select #4.1/D:47@NZ
1 atom, 1 residue, 1 model selected
> select #3/D:40@OG1
1 atom, 1 residue, 1 model selected
> select add #4.1/D:47@NZ
2 atoms, 2 residues, 2 models selected
> ui tool show Contacts
> contacts sel restrict both ignoreHiddenModels true select true
No contacts
> select #3/D:40@OG1
1 atom, 1 residue, 1 model selected
> select add #4.1/D:47@NZ
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #3/D:40@OG1 #4.1/D:47@NZ
Distance between DTHP_K40TQ47K_refine_026-coot-0.pdb #3/D THR 40 OG1 and
DTHP_K40TQ47K_refine_026-coot-0.pdb 0 0 0 sym 1 #4.1/D LYS 47 NZ: 3.13Å
> select clear
> select #3/E:47@NZ
1 atom, 1 residue, 1 model selected
> select add #4.1/C:40@CG2
2 atoms, 2 residues, 2 models selected
> distance #3/E:47@NZ #4.1/C:40@CG2
Distance between DTHP_K40TQ47K_refine_026-coot-0.pdb #3/E LYS 47 NZ and
DTHP_K40TQ47K_refine_026-coot-0.pdb 0 0 0 sym 1 #4.1/C THR 40 CG2: 9.36Å
> select clear
> save
> /Users/anushkaghosh/Documents/Documents/chimaera/DTHP_double_mutants/Q47KK40T-close.png
> width 1329 height 782 supersample 3 transparentBackground true
> ui windowfill toggle
> open /Users/anushkaghosh/Downloads/HTHP_bessy200319_C2221.pdb format pdb
Chain information for HTHP_bessy200319_C2221.pdb #10
---
Chain | Description
A B E | No description available
C D F | No description available
64 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open /Users/anushkaghosh/Downloads/HTHP_bessy200319_C2221.pdb format pdb
Chain information for HTHP_bessy200319_C2221.pdb #11
---
Chain | Description
A B E | No description available
C D F | No description available
64 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> show #!3,10-11#!4.1 cartoons
Computing secondary structure
> style #!3,10-11#!4.1 stick
Changed 30368 atom styles
> hide #!3,10-11#!4.1 atoms
> volume style surface
No volumes specified
> volume style mesh
No volumes specified
> view clip false
> save
> /Users/anushkaghosh/Documents/Documents/chimaera/DTHP_double_mutants/bleh.cxs
> hide #!4 models
> hide #!3 models
> hide #7 models
> hide #8 models
> select subtract #8
Nothing selected
> hide #!9 models
> hide #9.1 models
> ui tool show "Crystal Contacts"
> crystalcontacts #10 distance 1
1 pairs of asymmetric units of HTHP_bessy200319_C2221.pdb contact at distance
1.0 A
Atoms MTRIX SMTRY Unit cell MTRIXref Copies
2 0 2 0 0 -1 0 1
> select ::name="HEM"
5694 atoms, 5928 bonds, 312 pseudobonds, 78 residues, 26 models selected
> show sel & #!10-11#!2.1 atoms
> select clear
> select #10/A:43
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #10-11/A-F:40,47
468 atoms, 444 bonds, 24 residues, 2 models selected
> select #10,11/A-F:40,47
468 atoms, 444 bonds, 24 residues, 2 models selected
> crystalcontacts delete #10
> crystalcontacts #10 distance 1 rainbow false
1 pairs of asymmetric units of HTHP_bessy200319_C2221.pdb contact at distance
1.0 A
Atoms MTRIX SMTRY Unit cell MTRIXref Copies
2 0 2 0 0 -1 0 1
> select clear
> save
> /Users/anushkaghosh/Documents/Documents/chimaera/DTHP_double_mutants/bleh.cxs
===== 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 - 89.4
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.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: Mac mini
Model Identifier: Macmini9,1
Model Number: Z12N0006DD/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 3 days, 8 hours, 40 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL U2720Q:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 50.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
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 , 7 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 , 7 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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The ChimeraX crash report panel said what we know about this crash
"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."
The ChimeraX daily build is using a newer version of the Qt window toolkit that may fix these Mac multi-display crashes.