![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17205 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-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 0x00000001f0884f40 (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.pdb_lib._load_libs, 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, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree (total: 61)
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{
"uptime" : 250000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac15,12",
"coalitionID" : 7364,
"osVersion" : {
"train" : "macOS 14.6",
"build" : "23G80",
"releaseType" : "User"
},
"captureTime" : "2025-03-26 17:11:48.1953 +0100",
"codeSigningMonitor" : 1,
"incident" : "76871F46-9303-4C6D-BDC5-A3F5CBF2A9D8",
"pid" : 52412,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-25 20:35:31.8146 +0100",
"procStartAbsTime" : 5282227691383,
"procExitAbsTime" : 6174999418657,
"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":"74DC2FB7-DFB9-5D3B-92C7-63DE63B9BB3B","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E2021406-A73F-75E2-1BEE-B7EC748CF3F3",
"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" : 1,
"sleepWakeUUID" : "315D283B-8565-452C-A0C9-5E050F4EEB5D",
"sip" : "enabled",
"vmRegionInfo" : "0x13664eb62738 is not in any region. Bytes after previous region: 20849091815225 Bytes before following region: 84222988114120\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, 0x000013664eb62738","rawCodes":[1,21330128152376],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000013664eb62738"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":52412},
"vmregioninfo" : "0x13664eb62738 is not in any region. Bytes after previous region: 20849091815225 Bytes before following region: 84222988114120\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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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/sara.buscarini/Desktop/Phd/PDB/5il0.pdb
5il0.pdb title:
Crystal structural of the METTL3-METTL14 complex for N6-adenosine methylation
[more info...]
Chain information for 5il0.pdb #1
---
Chain | Description | UniProt
A | METTL3 | MTA70_HUMAN 369-580
B | methyltransferase-LIKE protein 14 | MET14_HUMAN 109-408
Non-standard residues in 5il0.pdb #1
---
BR — bromide ion
EDO — 1,2-ethanediol (ethylene glycol)
> color #1/A #f27a93ff
> color #1/B #fcbe7cff
> open /Users/sara.buscarini/Desktop/Phd/PDB/5il1.pdb
5il1.pdb title:
Crystal structure of sam-bound METTL3-METTL14 complex [more info...]
Chain information for 5il1.pdb #2
---
Chain | Description | UniProt
A | METTL3 | MTA70_HUMAN 369-580
B | methyltransferase-LIKE protein 14 | MET14_HUMAN 109-408
Non-standard residues in 5il1.pdb #2
---
EDO — 1,2-ethanediol (ethylene glycol)
SAM — S-adenosylmethionine
> hide #!1 models
> show #!2 surfaces
> select add #2
4336 atoms, 4102 bonds, 1 pseudobond, 828 residues, 2 models selected
> show sel cartoons
> color #2/A #f27a93ff
> show #!2 target m
> view #2 clip false
> hide sel surfaces
> select subtract #2
2 models selected
> color #2/B #fcbe7cff
> select #2/SAM
Nothing selected
> select #2/A:SAM
27 atoms, 29 bonds, 1 residue, 1 model selected
> color #2/A:SAM green
> style sel stick
Changed 27 atom styles
> color sel byhetero
> select #2/A:511
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:SAM
27 atoms, 29 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
18 hydrogen bonds found
> hbonds sel showDist true
18 hydrogen bonds found
> color #2/A:511 red
> ui tool show Distances
> select #2/A:511@OG
1 atom, 1 residue, 1 model selected
> select #2/A:601@OXT
1 atom, 1 residue, 1 model selected
> select add #2/A:511@OG
2 atoms, 2 residues, 1 model selected
> distance #2/A:601@OXT #2/A:511@OG
Distance between 5il1.pdb #2/A SAM 601 OXT and SER 511 OG: 4.585Å
> color #2/A:426 red
> color #2/A:411 red
> color #2/A:397 red
> select #2/A:397 red
Expected a keyword
> select #2/A:397 red
Expected a keyword
> select #2/A:397
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:397
7 atoms, 7 bonds, 1 residue, 1 model selected
> color #2/A:425 red
> select #2/A:425
8 atoms, 7 bonds, 1 residue, 1 model selected
> color #2/A:402 red
> color #2/A:516 red
> select #2/A:516
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:515
8 atoms, 7 bonds, 1 residue, 1 model selected
> color #2/A:515 red
> color #2/A:546 red
> color #2/A:4 red
> select #2/A:4
Nothing selected
> color #2/A:438 red
> open
> /Users/sara.buscarini/Desktop/ligands_METTL3:14/Antonio_Sara_ligands.cxs
opened ChimeraX session
> hide #!5 models
> ui tool show "Side View"
> select add #2
4336 atoms, 4102 bonds, 20 pseudobonds, 828 residues, 4 models selected
> select subtract #2
Nothing selected
> color #2/A:414 red
> color #2/A:534 orange
> color #2/A:409 green
> color #2/A:409 light green
> color #2/A:409 lightblue purple
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #2/A:397 purple
> open /Users/sara.buscarini/Desktop/Phd/PDB/mutatedM414I/5il1M414I.pdb
5il1M414I.pdb title:
Crystal structure of sam-bound METTL3-METTL14 complex [more info...]
Chain information for 5il1M414I.pdb #8
---
Chain | Description | UniProt
A | METTL3 | MTA70_HUMAN 369-580
B | methyltransferase-LIKE protein 14 | MET14_HUMAN 109-408
Non-standard residues in 5il1M414I.pdb #8
---
EDO — 1,2-ethanediol (ethylene glycol)
SAM — S-adenosylmethionine
> hide #7.1 models
> hide #!7 models
> hide #!2 models
> color #8/A #f27a93ff
> color #8/B #fcbe7cff
> color #8/A:SAM green
> select #8/A:SAM
27 atoms, 29 bonds, 1 residue, 1 model selected
> color sel byhetero
> select add #8
4336 atoms, 4102 bonds, 1 pseudobond, 828 residues, 2 models selected
> select subtract #8
Nothing selected
> select #8/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> color #8/A:414 red
> select #8/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> swapaa I #414:A
No amino acid residues specified for swapping
> swapaa I414M
Missing or invalid "residues" argument: invalid residues specifier
> swapaa #8/A:414
Missing or invalid "resTypes" argument: Expected a text string
> swapaa I @414:A
No amino acid residues specified for swapping
> swapaa #8/A:414 ile
Using Dunbrack library
5il1M414I.pdb #8/A MET 414: phi -65.1, psi -50.0 trans
Applying ILE rotamer (chi angles: -62.6 -60.5) to 5il1M414I.pdb #8/A ILE 414
> save /Users/sara.buscarini/Desktop/5il1M414I.pdb
> hide #!8 models
> show #!8 models
> save /Users/sara.buscarini/Desktop/5IL1mut.pdb
No model chosen to save relative to
> select add #8
4336 atoms, 4102 bonds, 1 pseudobond, 828 residues, 2 models selected
> select subtract #8
Nothing selected
> select add #8
4336 atoms, 4102 bonds, 1 pseudobond, 828 residues, 2 models selected
No model chosen to save relative to
> select subtract #8
Nothing selected
> open /Users/sara.buscarini/Desktop/Phd/PDB/mutatedM414I/5il1mut.pdb
Summary of feedback from opening
/Users/sara.buscarini/Desktop/Phd/PDB/mutatedM414I/5il1mut.pdb
---
warnings | Duplicate atom serial number found: 366
Duplicate atom serial number found: 367
Duplicate atom serial number found: 368
Duplicate atom serial number found: 369
Duplicate atom serial number found: 370
3 messages similar to the above omitted
5il1mut.pdb title:
Crystal structure of sam-bound METTL3-METTL14 complex [more info...]
Chain information for 5il1mut.pdb #9
---
Chain | Description | UniProt
A | METTL3 | MTA70_HUMAN 369-580
B | methyltransferase-LIKE protein 14 | MET14_HUMAN 109-408
Non-standard residues in 5il1mut.pdb #9
---
EDO — 1,2-ethanediol (ethylene glycol)
SAM — S-adenosylmethionine
> hide #!9 models
> select add #9
4336 atoms, 4102 bonds, 1 pseudobond, 828 residues, 2 models selected
> show #!9 models
> hide #!9 models
> select subtract #9
Nothing selected
> open /Users/sara.buscarini/Desktop/5il0-coot-0.pdb
5il0-coot-0.pdb title:
Crystal structural of the METTL3-METTL14 complex for N6-adenosine methylation
[more info...]
Chain information for 5il0-coot-0.pdb #10
---
Chain | Description | UniProt
A | METTL3 | MTA70_HUMAN 369-580
B | methyltransferase-LIKE protein 14 | MET14_HUMAN 109-408
Non-standard residues in 5il0-coot-0.pdb #10
---
BR — bromide ion
EDO — 1,2-ethanediol (ethylene glycol)
> hide #!8 models
> select add #10
4347 atoms, 4115 bonds, 7 pseudobonds, 827 residues, 2 models selected
> show sel cartoons
> show sel surfaces
> hide sel surfaces
> select add #10
4347 atoms, 4115 bonds, 7 pseudobonds, 827 residues, 6 models selected
> select subtract #10
2 models selected
> select #10/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!5 models
> hide #!10 models
> show #!5 surfaces
> select add #5
3648 atoms, 3719 bonds, 5 pseudobonds, 464 residues, 4 models selected
> show target m
> hide #!5 models
> hide #!9 models
> hide #!10 models
> hide #!8 models
> hide #7.1 models
> hide #!7 models
> show #!5 models
> hide #!6 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> hide sel & #!5 surfaces
> select add #4
7370 atoms, 7319 bonds, 9 pseudobonds, 1130 residues, 8 models selected
> select add #5
7370 atoms, 7319 bonds, 9 pseudobonds, 1130 residues, 10 models selected
> select subtract #4
3648 atoms, 3719 bonds, 5 pseudobonds, 464 residues, 8 models selected
> select subtract #5
8 atoms, 7 bonds, 1 residue, 4 models selected
> select #5/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> color #5/A:414 f27a93ff
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #8/A #f27a93ff
> color #5/A #f27a93ff
> color #5/A:414 #f27a93ff
> color #5/A:414 red
> select #5/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> style sel stick
Changed 8 atom styles
> style sel stick
Changed 8 atom styles
> show sel cartoons
> style sel stick
Changed 8 atom styles
> style sel ball
Changed 8 atom styles
> style sel sphere
Changed 8 atom styles
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel cartoons
> style sel stick
Changed 8 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> hide sel surfaces
> show sel surfaces
> hide sel cartoons
> show sel cartoons
> undo
> style sel ball
Changed 8 atom styles
> style sel ball
Changed 8 atom styles
> style sel sphere
Changed 8 atom styles
> select #5/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel surfaces
> style sel stick
Changed 8 atom styles
> show sel cartoons
> style sel stick
Changed 8 atom styles
> style sel stick
Changed 8 atom styles
> style sel stick
Changed 8 atom styles
> select #5/A:416
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> style sel stick
Changed 11 atom styles
> color sel byhetero
> show sel cartoons
> style sel stick
Changed 11 atom styles
> style sel sphere
Changed 11 atom styles
> hide sel atoms
> show sel atoms
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> style sel stick
Changed 11 atom styles
> show (#!5 & sel) target ab
> undo
> select #5/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (#!5 & sel) target ab
> color sel byhetero
> select #5/A:398
14 atoms, 15 bonds, 1 residue, 1 model selected
> show (#!5 & sel) target ab
> color sel byhetero
> color #5/A:398 light blue
> color sel byhetero
> color #5/A:398 blue
> color sel byhetero
> color #5/A:396 pink
> select #5/A:396 pink
Expected a keyword
> select #5/A:396
7 atoms, 7 bonds, 1 residue, 1 model selected
> show (#!5 & sel) target ab
> color sel byhetero
> select #5/A:378
8 atoms, 7 bonds, 1 residue, 1 model selected
> color #5/A:378 purple
> color sel byhetero
> select #5/A:378
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #5/A:377ù
Expected an objects specifier or a keyword
> select #5/A:377
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:378
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> hide #10.3 models
> hide #10.2 models
> hide #10.1 models
> close #9
> close #10
> close #8
> select add #5
3640 atoms, 3712 bonds, 5 pseudobonds, 463 residues, 5 models selected
> select subtract #5
2 models selected
> open /Users/sara.buscarini/Desktop/mutated_proteins/7o2i-coot-0.pdb
7o2i-coot-0.pdb title:
METTL3-METTL14 heterodimer bound to the sam competitive small molecule
inhibitor STM2457 [more info...]
Chain information for 7o2i-coot-0.pdb #8
---
Chain | Description | UniProt
A | N6-adenosine-methyltransferase catalytic subunit | MTA70_HUMAN 354-580
B | N6-adenosine-methyltransferase non-catalytic subunit | MET14_HUMAN 107-395
Non-standard residues in 7o2i-coot-0.pdb #8
---
DMS — dimethyl sulfoxide
V22 —
~{N}-[[6-[(cyclohexylmethylamino)methyl]imidazo[1,2-A]pyridin-2-yl]methyl]-4-oxidanylidene-1~{H}-pyrido[1,2-A]pyrimidine-2-carboxamide
> hide #!5 models
> color #8/A #f27a93ff
> color #8/B #fcbe7cff
> color #8/A:V22 green
> select #8/A:V22
33 atoms, 37 bonds, 1 residue, 1 model selected
> color #8/A:414 red
> select #8/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> swapaa #8/A:414 ileA
Using Dunbrack library
7o2i-coot-0.pdb #8/A ILE 414: phi -70.9, psi -57.3 trans
Dunbrack rotamer library does not support ILEA
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> close #8
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> color #5/A #f27a93ff
> color #5/B #fcbe7cff
> color #5/A:V22 green
> select #5/A:V22
33 atoms, 37 bonds, 1 residue, 1 model selected
> color #5/A:414 red
> select #5/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:V22
33 atoms, 37 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #5/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> style sel stick
Changed 8 atom styles
> show (#!5 & sel) target ab
> color #5/A #f27a93ff
> color #5/B #fcbe7cff
> color #5/A:V22 green
> select #5/A:V22
33 atoms, 37 bonds, 1 residue, 1 model selected
> color #5/A:414 red
> select #5/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> color #5/A:398 blue
> select #5/A:398
14 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> select #5/A:396 light pink
Expected a keyword
> select #5/A:396
7 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> select #5/A:378 purple
Expected a keyword
> select #5/A:378
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> color #5/A #f27a93ff
> color #5/B #fcbe7cff
> color #5/A:V22 green
> select #5/A:V22
33 atoms, 37 bonds, 1 residue, 1 model selected
> color #5/A:414 red
> select #5/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> color #5/A:398 blue
> select #5/A:398
14 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> Color #5/A:396 light pink
Unknown command: Color #5/A:396 light pink
> select #5/A:396
7 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> Color #5/A:378 purple
Unknown command: Color #5/A:378 purple
> select #5/A:378
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> color #5/A #f27a93ff
> color #5/B #fcbe7cff
> color #5/A:V22 green
> select #5/A:V22
33 atoms, 37 bonds, 1 residue, 1 model selected
> color #5/A:414 red
> select #5/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> color #5/A:398 blue
> select #5/A:398
14 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> color #5/A:396 light pink
> select #5/A:396
7 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> color #5/A:378 purple
> select #5/A:378
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show (#!5 & sel) target ab
> select add #5
3640 atoms, 3712 bonds, 5 pseudobonds, 463 residues, 3 models selected
> select subtract #5
2 models selected
> select #5/A:V22
33 atoms, 37 bonds, 1 residue, 1 model selected
> color sel byhetero
> select add #5
3640 atoms, 3712 bonds, 5 pseudobonds, 463 residues, 2 models selected
> select subtract #5
2 models selected
> select #5/A:378
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> select #5/A:396
7 atoms, 7 bonds, 1 residue, 1 model selected
> show (#!5 & sel) target ab
> select #5/A:398
14 atoms, 15 bonds, 1 residue, 1 model selected
> show (#!5 & sel) target ab
> select add #5
3640 atoms, 3712 bonds, 5 pseudobonds, 463 residues, 3 models selected
> select subtract #5
2 models selected
> view name glutamate_role
> view_nameV22
Unknown command: view_nameV22
> view_name
Unknown command: view_name
> view name V22
> save /Users/sara.buscarini/Desktop/1.png width 987 height 646 supersample 3
> transparentBackground true
> open /Users/sara.buscarini/Desktop/mutated_proteins/7o2i-coot-0.pdb
7o2i-coot-0.pdb title:
METTL3-METTL14 heterodimer bound to the sam competitive small molecule
inhibitor STM2457 [more info...]
Chain information for 7o2i-coot-0.pdb #8
---
Chain | Description | UniProt
A | N6-adenosine-methyltransferase catalytic subunit | MTA70_HUMAN 354-580
B | N6-adenosine-methyltransferase non-catalytic subunit | MET14_HUMAN 107-395
Non-standard residues in 7o2i-coot-0.pdb #8
---
DMS — dimethyl sulfoxide
V22 —
~{N}-[[6-[(cyclohexylmethylamino)methyl]imidazo[1,2-A]pyridin-2-yl]methyl]-4-oxidanylidene-1~{H}-pyrido[1,2-A]pyrimidine-2-carboxamide
> hide #!5 models
> color #8/A #f27a93ff
> color #8/B #fcbe7cff
> color #8/A:V22 green
> select #8/A:V22
33 atoms, 37 bonds, 1 residue, 1 model selected
> color #8/A:414 red
> select #8/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> color #8/A:398 blue
> select #8/A:398
14 atoms, 15 bonds, 1 residue, 1 model selected
> style set stick
Expected a keyword
> color #8/A:396 light pink
> select #5/A:396
7 atoms, 7 bonds, 1 residue, 1 model selected
> show (#!5 & sel) target ab
> color #8/A:378 purple
> select #8/A:378
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> select #8/A:V22
33 atoms, 37 bonds, 1 residue, 1 model selected
> style sel stick
Changed 33 atom styles
> select #8/A:V22
33 atoms, 37 bonds, 1 residue, 1 model selected
> color sel byhetero
> select add #8
3640 atoms, 3709 bonds, 33 pseudobonds, 463 residues, 2 models selected
> select subtract #8
Nothing selected
> select #8/A:443
6 atoms, 5 bonds, 1 residue, 1 model selected
> color #8/A:443 water green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #8/A:443 light green
> color #8/A #f27a93ff
> color #8/B #fcbe7cff
> color #8/A:V22 green
> select #8/A:V22
33 atoms, 37 bonds, 1 residue, 1 model selected
> color #8/A:414 red
> select #8/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> color #8/A:398 blue
> select #8/A:398
14 atoms, 15 bonds, 1 residue, 1 model selected
> show (#!5 & sel) target ab
> color #8/A:396 light pink
> select #5/A:396
7 atoms, 7 bonds, 1 residue, 1 model selected
> show (#!5 & sel) target ab
> color #8/A:378 purple
> select #8/A:378
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (#!5 & sel) target ab
> select #8/A:V22
33 atoms, 37 bonds, 1 residue, 1 model selected
> show (#!5 & sel) target ab
> select #8/A:V22
33 atoms, 37 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #8/A:443
6 atoms, 5 bonds, 1 residue, 1 model selected
> color #8/A:443 water green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #8/A #f27a93ff
> color #8/B #fcbe7cff
> color #8/A:V22 green
> select #8/A:V22
33 atoms, 37 bonds, 1 residue, 1 model selected
> color #8/A:414 red
> select #8/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> color #8/A:398 blue
> select #8/A:398
14 atoms, 15 bonds, 1 residue, 1 model selected
> show (#!5 & sel) target ab
> color #8/A:396 light pink
> select #5/A:396
7 atoms, 7 bonds, 1 residue, 1 model selected
> show (#!5 & sel) target ab
> color #8/A:378 purple
> select #8/A:378
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (#!5 & sel) target ab
> select #8/A:V22
33 atoms, 37 bonds, 1 residue, 1 model selected
> show (#!5 & sel) target ab
> select #8/A:V22
33 atoms, 37 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #8/A:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select #8/A:398
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel target ab
> select #8/A:396
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select add #8
3640 atoms, 3709 bonds, 33 pseudobonds, 463 residues, 2 models selected
> select subtract #8
Nothing selected
> select #8/A:443
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> color #8/A:414 light blue
> undo
> color #8/A:443 light blue
> select add #8
3640 atoms, 3709 bonds, 33 pseudobonds, 463 residues, 2 models selected
> select subtract #8
Nothing selected
> save /Users/sara.buscarini/Desktop/2.png width 987 height 619 supersample 3
> transparentBackground true
> show #!5 models
> show #!4 models
> hide #!4 models
> hide #!8 models
> show #!8 models
> hide #!5 models
> show #!5 models
> hide #!8 models
> color #8/A:396 yellow
> color #5/A:396 yellow
> view name glutamate_role
> save /Users/sara.buscarini/Desktop/7o2i_new.png width 1437 height 903
> supersample 3 transparentBackground true
> save /Users/sara.buscarini/Desktop/1.png width 1437 height 903 supersample 3
> transparentBackground true
> show #!8 models
> hide #!5 models
> select add #8
3640 atoms, 3709 bonds, 33 pseudobonds, 463 residues, 2 models selected
> show #!8 target m
> show sel surfaces
> hide sel surfaces
> select add #8
3640 atoms, 3709 bonds, 33 pseudobonds, 463 residues, 5 models selected
> select subtract #8
2 models selected
> save /Users/sara.buscarini/Desktop/7o2i_M414I.png width 1437 height 903
> supersample 3 transparentBackground true
> show #!5 models
> hide #!8 models
> save /Users/sara.buscarini/Desktop/mut.png width 1437 height 903 supersample
> 3 transparentBackground true
> show #!8 models
> hide #!5 models
> view #8 clip false
> select #8/A:443
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show Distances
> select #8/A:443@SG
1 atom, 1 residue, 1 model selected
> select #8/A:414@CG2
1 atom, 1 residue, 1 model selected
> select add #8/A:443@SG
2 atoms, 2 residues, 2 models selected
> distance #8/A:414@CG2 #8/A:443@SG
Distance between 7o2i-coot-0.pdb #8/A ILE 414 CG2 and CYS 443 SG: 2.954Å
> distance #8/A:414@CG2 #8/A:443@SG
Distance already exists; modify distance properties with 'distance style'
> distance #8/A:414@CG2 #8/A:443@SG
Distance already exists; modify distance properties with 'distance style'
> show #!7 models
> show #7.1 models
> show #!5 models
> hide #!7 models
> hide #7.1 models
> show #7.1 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #7.1 models
> hide #!8 models
> select add #8
3640 atoms, 3709 bonds, 34 pseudobonds, 463 residues, 4 models selected
> select #8/A:443
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:443
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> olor #5/A:443 light blue
Unknown command: olor #5/A:443 light blue
> color #5/A:443 light blue
> select #5/A:414@CE
1 atom, 1 residue, 1 model selected
> select add #5/A:443@SG
2 atoms, 2 residues, 2 models selected
> distance #5/A:414@CE #5/A:443@SG
Distance between 7o2i.pdb #5/A MET 414 CE and CYS 443 SG: 5.168Å
> show #7.1 models
Unsupported scale factor (0.000000) detected on Display0
> show #!8 models
> hide #7.1 models
> hide #!7 models
> hide #!5 models
> show #7.1 models
> hide #!7 models
> show #!7 models
> show #!5 models
> hide #!7 models
> hide #7.1 models
> hide #!8 models
Unsupported scale factor (0.000000) detected on Display0
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Unsupported scale factor (0.000000) detected on Display0
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> view #7 clip false
No displayed objects specified.
> view #7 clip false
No displayed objects specified.
> show #!8 models
> view #8 clip false
> hide #!5 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #7.1 models
> show #!5 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> hide #7.1 models
> hide #!7 models
> show #!7 models
> show #7.1 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac15,12
Model Number: Z1B8001FCT/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6 (23G80)
Kernel Version: Darwin 23.6.0
Time since boot: 7 days, 20 hours, 29 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
T27p-30:
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
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 7 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 , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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