![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17387 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-15.4-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 0x0000000202968c40 (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.surface._surface, 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.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, fontTools.misc.bezierTools, lxml._elementpath, lxml.etree, fontTools.varLib.iup, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 64)
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"procRole" : "Foreground",
"version" : 2,
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"modelCode" : "Mac15,7",
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"codeSigningMonitor" : 1,
"incident" : "A518FCDE-3B82-4564-86D6-3526BF6C1BD9",
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"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-15 12:05:59.8013 -0400",
"procStartAbsTime" : 1180955747704,
"procExitAbsTime" : 1713902257135,
"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" : "BD1308D5-7C1C-C889-AD39-6908BB6F1170",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "CEA7AC2C-1569-42F1-A274-0FE959CE4309",
"wakeTime" : 25814,
"sleepWakeUUID" : "6C2EFDDE-8399-48C4-AB8A-5A9D69CB41CF",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4300029591\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1004d4000-1004d8000 [ 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":55076},
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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/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_7ZA1_mono.pdb
> open
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_7ZA1_mono.pdb
> format pdb
> open
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft_monomer.pdb
> open /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/UNC5D_5fft.pdb
Chain information for UNC5D_5fft.pdb #1
---
Chain | Description
A E | No description available
B F | No description available
C D G H | No description available
> show atoms
> show cartoons
> hide atoms
> close session
> open
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft.pdb
Summary of feedback from opening
/Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 91 HIS A 95 1 5
Start residue of secondary structure not found: HELIX 2 2 THR A 117 ASP A 123
1 7
Start residue of secondary structure not found: HELIX 3 3 ALA B 82 VAL B 87 1
6
Start residue of secondary structure not found: HELIX 4 4 SER B 125 LEU B 132
1 8
Start residue of secondary structure not found: HELIX 5 5 ALA B 154 ALA B 158
1 5
26 messages similar to the above omitted
End residue of secondary structure not found: SHEET 4 4 1 GLN A 80 CYS A 85 0
End residue of secondary structure not found: SHEET 5 5 1 GLU A 88 TRP A 89 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 96 GLU A 98
0
Start residue of secondary structure not found: SHEET 7 7 1 ARG A 110 PHE A
113 0
Start residue of secondary structure not found: SHEET 8 8 1 TRP A 131 TRP A
137 0
Start residue of secondary structure not found: SHEET 9 9 1 THR A 142 LYS A
144 0
Start residue of secondary structure not found: SHEET 10 10 1 ALA A 148 SER A
149 0
161 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (73 )
Cannot find LINK/SSBOND residue CYS (85 )
Cannot find LINK/SSBOND residue CYS (178 )
Cannot find LINK/SSBOND residue CYS (262 )
Cannot find LINK/SSBOND residue CYS (266 )
69 messages similar to the above omitted
Chain information for modeller_UNC5D_5fft.pdb #1
---
Chain | Description
A E | No description available
Computing secondary structure
> close
> open
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_7ZA1.pdb
Summary of feedback from opening
/Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_7ZA1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 91 HIS A 95 1 5
Start residue of secondary structure not found: HELIX 2 2 THR A 117 ASP A 123
1 7
Start residue of secondary structure not found: HELIX 3 3 ALA B 82 VAL B 87 1
6
Start residue of secondary structure not found: HELIX 4 4 SER B 125 LEU B 132
1 8
Start residue of secondary structure not found: HELIX 5 5 ALA B 154 ALA B 158
1 5
26 messages similar to the above omitted
End residue of secondary structure not found: SHEET 4 4 1 GLN A 80 CYS A 85 0
End residue of secondary structure not found: SHEET 5 5 1 GLU A 88 TRP A 89 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 96 GLU A 98
0
Start residue of secondary structure not found: SHEET 7 7 1 ARG A 110 PHE A
113 0
Start residue of secondary structure not found: SHEET 8 8 1 TRP A 131 TRP A
137 0
Start residue of secondary structure not found: SHEET 9 9 1 THR A 142 LYS A
144 0
Start residue of secondary structure not found: SHEET 10 10 1 ALA A 148 SER A
149 0
161 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (73 )
Cannot find LINK/SSBOND residue CYS (85 )
Cannot find LINK/SSBOND residue CYS (178 )
Cannot find LINK/SSBOND residue CYS (262 )
Cannot find LINK/SSBOND residue CYS (266 )
69 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 1 1 HIS A 91 HIS A 95 1
5
Start residue of secondary structure not found: HELIX 2 2 THR A 117 ASP A 123
1 7
Start residue of secondary structure not found: HELIX 3 3 ALA B 82 VAL B 87 1
6
Start residue of secondary structure not found: HELIX 4 4 SER B 125 LEU B 132
1 8
Start residue of secondary structure not found: HELIX 5 5 ALA B 154 ALA B 158
1 5
111 messages similar to the above omitted
End residue of secondary structure not found: SHEET 89 89 1 GLN E 80 CYS E 85
0
End residue of secondary structure not found: SHEET 90 90 1 GLU E 88 TRP E 89
0
Start residue of secondary structure not found: SHEET 91 91 1 VAL E 96 LEU E
101 0
Start residue of secondary structure not found: SHEET 92 92 1 LYS E 108 ILE E
114 0
Start residue of secondary structure not found: SHEET 93 93 1 TRP E 131 TRP E
137 0
Start residue of secondary structure not found: SHEET 94 94 1 THR E 142 LYS E
144 0
Start residue of secondary structure not found: SHEET 95 95 1 ALA E 148 SER E
149 0
24 messages similar to the above omitted
End residue of secondary structure not found: SHEET 120 120 1 ARG F 280 ASP F
282 0
Start residue of secondary structure not found: SHEET 121 121 1 GLN F 304 THR
F 306 0
Start residue of secondary structure not found: SHEET 122 122 1 TRP F 312 PHE
F 313 0
Start residue of secondary structure not found: SHEET 123 123 1 ASN F 333 ARG
F 335 0
Start residue of secondary structure not found: SHEET 124 124 1 CYS F 339 GLY
F 341 0
Start residue of secondary structure not found: SHEET 125 125 1 ARG G 99 CYS G
104 0
46 messages similar to the above omitted
Chain information for modeller_UNC5D_7ZA1.pdb
---
Chain | Description
1.1/A 1.1/E 1.2/E 1.2/F 1.2/G 1.2/H | No description available
Computing secondary structure
> hide #1.2 models
> close #1.2
> select add #1.1
6574 atoms, 6658 bonds, 420 residues, 1 model selected
> select subtract #1.1
Nothing selected
> Selecty /A
Unknown command: Selecty /A
> Selecty #1/A
Unknown command: Selecty #1/A
> Select #1/A
Unknown command: Select #1/A
> Select #1/A
Unknown command: Select #1/A
> Select #/A
Unknown command: Select #/A
> Select /A
Unknown command: Select /A
> Select #1.1/A
Unknown command: Select #1.1/A
> select /A
3287 atoms, 3329 bonds, 210 residues, 1 model selected
> select /E
3287 atoms, 3329 bonds, 210 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /A
3287 atoms, 3329 bonds, 210 residues, 1 model selected
> save
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_7ZA1_monomer.pdb
> close session
> open
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_7ZA1_monomer.pdb
> format pdb
Chain information for modeller_UNC5D_7ZA1_monomer.pdb #1
---
Chain | Description
A | No description available
> open
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft_monomer.pdb
> select add #1
3287 atoms, 3329 bonds, 210 residues, 1 model selected
> select subtract #1
Nothing selected
> close session
> open
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft_monomer.pdb
> open
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft.pdb
Summary of feedback from opening
/Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 91 HIS A 95 1 5
Start residue of secondary structure not found: HELIX 2 2 THR A 117 ASP A 123
1 7
Start residue of secondary structure not found: HELIX 3 3 ALA B 82 VAL B 87 1
6
Start residue of secondary structure not found: HELIX 4 4 SER B 125 LEU B 132
1 8
Start residue of secondary structure not found: HELIX 5 5 ALA B 154 ALA B 158
1 5
26 messages similar to the above omitted
End residue of secondary structure not found: SHEET 4 4 1 GLN A 80 CYS A 85 0
End residue of secondary structure not found: SHEET 5 5 1 GLU A 88 TRP A 89 0
Start residue of secondary structure not found: SHEET 6 6 1 VAL A 96 GLU A 98
0
Start residue of secondary structure not found: SHEET 7 7 1 ARG A 110 PHE A
113 0
Start residue of secondary structure not found: SHEET 8 8 1 TRP A 131 TRP A
137 0
Start residue of secondary structure not found: SHEET 9 9 1 THR A 142 LYS A
144 0
Start residue of secondary structure not found: SHEET 10 10 1 ALA A 148 SER A
149 0
161 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (73 )
Cannot find LINK/SSBOND residue CYS (85 )
Cannot find LINK/SSBOND residue CYS (178 )
Cannot find LINK/SSBOND residue CYS (262 )
Cannot find LINK/SSBOND residue CYS (266 )
69 messages similar to the above omitted
Chain information for modeller_UNC5D_5fft.pdb #1
---
Chain | Description
A E | No description available
Computing secondary structure
> select /E
3287 atoms, 3329 bonds, 210 residues, 1 model selected
> select /A
3287 atoms, 3329 bonds, 210 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /E
3287 atoms, 3329 bonds, 210 residues, 1 model selected
> save
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft_monomer.pdb
> selectedOnly true relModel #1
> open
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_7ZA1_monomer.pdb
Chain information for modeller_UNC5D_7ZA1_monomer.pdb #2
---
Chain | Description
A | No description available
> hide #1 models
> show #1 models
> select subtract #1
Nothing selected
> hide #1 models
> show #1 models
> ui tool show Matchmaker
> matchmaker #2 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 modeller_UNC5D_5fft.pdb, chain E (#1) with
modeller_UNC5D_7ZA1_monomer.pdb, chain A (#2), sequence alignment score =
1031.1
RMSD between 197 pruned atom pairs is 1.081 angstroms; (across all 210 pairs:
1.890)
> hide #1 models
> show #1 models
> hide #1 models
> hide #2 models
> show #2 models
> show #1 models
> select add #1
3287 atoms, 3329 bonds, 210 residues, 1 model selected
> select subtract #1
Nothing selected
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> ui tool show Rotamers
Populating font family aliases took 70 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
No residues selected
> select add #2
3287 atoms, 3329 bonds, 210 residues, 1 model selected
> swapaa interactive sel ALA rotLib Dunbrack
No rotamers for ALA in Dunbrack rotamer library
> ui tool show Rotamers
> swapaa interactive sel ALA rotLib Dunbrack
No rotamers for ALA in Dunbrack rotamer library
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
modeller_UNC5D_7ZA1_monomer.pdb #2/A PRO 1: phi none, psi 9.5 trans
Changed 648 bond radii
> clashes #!2 & ~#!2/A:1 & ~solvent radius 0.075 reveal true restrict #2.1 &
> ~@c,ca,n
83 clashes
> hide sel atoms
> show sel cartoons
> clashes #!2 & ~#!2/A:1 & ~solvent radius 0.075 reveal true restrict #2.1 &
> ~@c,ca,n
83 clashes
> hide sel atoms
> close session
> open
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft_monomer.pdb
Chain information for modeller_UNC5D_5fft_monomer.pdb #1
---
Chain | Description
E | No description available
> open
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_7ZA1_monomer.pdb
Chain information for modeller_UNC5D_7ZA1_monomer.pdb #2
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2 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 modeller_UNC5D_5fft_monomer.pdb, chain E (#1) with
modeller_UNC5D_7ZA1_monomer.pdb, chain A (#2), sequence alignment score =
1031.1
RMSD between 197 pruned atom pairs is 1.081 angstroms; (across all 210 pairs:
1.890)
> matchmaker #2 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 modeller_UNC5D_5fft_monomer.pdb, chain E (#1) with
modeller_UNC5D_7ZA1_monomer.pdb, chain A (#2), sequence alignment score =
1031.1
RMSD between 197 pruned atom pairs is 1.081 angstroms; (across all 210 pairs:
1.890)
> hide #1 models
> close #1
> close
> open
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft_monomer.pdb
Chain information for modeller_UNC5D_5fft_monomer.pdb #1
---
Chain | Description
E | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain /E
Alignment identifier is 1/E
> select /E:211
16 atoms, 16 bonds, 1 residue, 1 model selected
> select /E
3287 atoms, 3329 bonds, 210 residues, 1 model selected
> save /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/5fft_monomer
> format fasta alignment 1/E
> hide sel atoms
> close session
> open 5fft
Summary of feedback from opening 5fft fetched from pdb
---
notes | Fetching compressed mmCIF 5fft from http://files.rcsb.org/download/5fft.cif
Fetching CCD SME from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/SME/SME.cif
5fft title:
Crystal Structure of Surfactant Protein-A Y221A Mutant [more info...]
Chain information for 5fft #1
---
Chain | Description | UniProt
A | Pulmonary surfactant-associated protein A | SFTPA_RAT 81-228
Non-standard residues in 5fft #1
---
CA — calcium ion
5fft mmCIF Assemblies
---
1| author_and_software_defined_assembly
21 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close session
> open 5FTT
5ftt title:
Octameric complex of Latrophilin 3 (Lec, Olf) , Unc5D (Ig, Ig2, TSP1) and
FLRT2 (LRR) [more info...]
Chain information for 5ftt #1
---
Chain | Description | UniProt
A E | NETRIN RECEPTOR UNC5D | UNC5D_RAT 32-307
B F | LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN FLRT2 | FLRT2_MOUSE 35-362
C D G H | ADHESION G PROTEIN-COUPLED RECEPTOR L3 | AGRL3_MOUSE 92-463
Non-standard residues in 5ftt #1
---
CA — calcium ion
NA — sodium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> show cartoons
> hide atoms
> select /F:36-367
2641 atoms, 2698 bonds, 332 residues, 1 model selected
> Select #1
Unknown command: Select #1
> Select all
Unknown command: Select all
> select clear
> interfaces ~solvent
14 buried areas: A E 1488, C B 841, G F 803, G H 712, C D 673, B A 626, C A
623, F E 619, G E 618, B D 580, F H 544, B E 485, F A 480, G C 328
> select /A:46-307
2060 atoms, 2115 bonds, 262 residues, 1 model selected
> select clear
> select /E:45-303
2041 atoms, 2096 bonds, 259 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A /E
Alignment identifier is 1
> select clear
> select /A,E:53
20 atoms, 20 bonds, 2 residues, 1 model selected
> select /A,E:53-65
226 atoms, 232 bonds, 26 residues, 1 model selected
> select /A:304-307/E:45
33 atoms, 33 bonds, 5 residues, 1 model selected
> select /E:45
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:46-52/E:45-52
95 atoms, 98 bonds, 15 residues, 1 model selected
> select clear
> sequence update /A
> close session
> open 5FTT
5ftt title:
Octameric complex of Latrophilin 3 (Lec, Olf) , Unc5D (Ig, Ig2, TSP1) and
FLRT2 (LRR) [more info...]
Chain information for 5ftt #1
---
Chain | Description | UniProt
A E | NETRIN RECEPTOR UNC5D | UNC5D_RAT 32-307
B F | LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN FLRT2 | FLRT2_MOUSE 35-362
C D G H | ADHESION G PROTEIN-COUPLED RECEPTOR L3 | AGRL3_MOUSE 92-463
Non-standard residues in 5ftt #1
---
CA — calcium ion
NA — sodium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> hide atoms
> show atoms
> show cartoons
> hide atoms
> select /B:36-361
2587 atoms, 2642 bonds, 326 residues, 1 model selected
> select /F:36-367
2641 atoms, 2698 bonds, 332 residues, 1 model selected
> select /C:100-464
2943 atoms, 3026 bonds, 365 residues, 1 model selected
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> select /C:100-464
2943 atoms, 3026 bonds, 365 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /D:202-464
2131 atoms, 2191 bonds, 263 residues, 1 model selected
> Delete
Unknown command: Delete
> delete atoms sel
> delete bonds sel
> select /G:97-464
2968 atoms, 3051 bonds, 368 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /H:202-462
2119 atoms, 2179 bonds, 261 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> interfaces ~solvent
5 buried areas: A E 1488, B A 626, F E 619, B E 485, F A 480
> color red
> undo
> color sel red
> color sel hot pink
> show sel atoms
> hide sel atoms
> show sel atoms
> show sel cartoons
> hide sel atoms
> undo
> redo
> select add #1
9449 atoms, 9669 bonds, 1195 residues, 1 model selected
> select subtract #1
Nothing selected
> view
> ui tool show "Side View"
> style sphere
Changed 9449 atom styles
> style stick
Changed 9449 atom styles
> show surfaces
Cell requested for row 0 is out of bounds for table with 2 rows! Resizing
table model.
> show cartoons
> hide surfaces
> hide atoms
> color (#!1 & sel) red
> color (#!1 & sel) hot pink
> select clear
> view
> select clear
> color (#!1 & sel) hot pink
> color (#!1 & sel) red
> color (#!1 & sel) hot pink
> ui tool show "Selection Inspector"
> save /Users/nirakar.basnet/Desktop/image1.png supersample 3
> show sel atoms
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> show sel atoms
> select clear
> show cartoons
> hide cartoons
> show surfaces
> color #1.2 #e0f4c1ff
> color #1.2 black
> color #1.2 #cadcaeff
> color #1.3 #d3ffe4ff
> color #1.5 black
> color #1.5 #d8ffe4ff
> color #1.5 #d8ffe400
> color #1.5 #d8ffe43e
> color #1.5 #d8ffe400
> color #1.5 #d8ffe491
> color #1.5 #d8ffe4f7
> hide surfaces
> show cartoons
> style stick
Changed 9449 atom styles
> hide atoms
> ui windowfill toggle
> show surfaces
> hide surfaces
> save /Users/nirakar.basnet/Desktop/image2.png supersample 3
> interfaces #1/A #1/F #1/E #1/F
3 buried areas: A E 1488, F E 619, F A 480
> select /B/F
5256 atoms, 5370 bonds, 660 residues, 1 model selected
> select /A/E
4157 atoms, 4271 bonds, 525 residues, 1 model selected
Drag select of 1179 residues
> save
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D_2/UNC5D_5FTT_FLRT_UNC_tetramer.pdb
> selectedOnly true relModel #1
> select clear
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style stick
Changed 9449 atom styles
> style stick
Changed 9449 atom styles
> style sphere
Changed 9449 atom styles
> hide cartoons
> show cartoons
> show surfaces
> save /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D_2/unc_prep.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 M3 Pro
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: MacBook Pro
Model Identifier: Mac15,7
Model Number: Z1AK0014ELL/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 36 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4 (24E248)
Kernel Version: Darwin 24.4.0
Time since boot: 1 day, 23 hours, 58 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
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
DELL P2417H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
27B2:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
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 , 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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