![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 16 months ago
Closed 16 months ago
#15671 closed defect (duplicate)
Crash waking Mac up 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-14.5-arm64-arm-64bit
ChimeraX Version: 1.8rc202406060152 (2024-06-06 01:52:35 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 0x00000001e9a2cc00 (most recent call first):
File "/Applications/ChimeraX-1.8-rc2024.06.06.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-rc2024.06.06.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-rc2024.06.06.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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, 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.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, 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, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 119)
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{
"uptime" : 730000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 64997,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-07-25 09:44:27.9398 +0530",
"codeSigningMonitor" : 1,
"incident" : "954BC643-B046-46DA-A9E1-72B8113BDE1D",
"pid" : 20165,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-07-25 05:26:40.1113 +0530",
"procStartAbsTime" : 17602764595885,
"procExitAbsTime" : 17737081477584,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8-rc2024.06.06.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B7BAE528-8A5E-6FAB-10DE-64DEB5E51B47",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"sleepWakeUUID" : "18D19972-AC65-4E30-B97A-DFB99B2CF2B4",
"sip" : "enabled",
"vmRegionInfo" : "0xbd25843d8c8 is not in any region. Bytes after previous region: 12517015541961 Bytes before following region: 92555064387384\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, 0x00008bd25843d8c8","rawCodes":[1,153735540234440],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00008bd25843d8c8 -> 0x00000bd25843d8c8 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":20165},
"vmregioninfo" : "0xbd25843d8c8 is not in any region. Bytes after previous region: 12517015541961 Bytes before following region: 92555064387384\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: 1.8rc202406060152 (2024-06-06)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/shruthi/Library/CloudStorage/Dropbox/Desmosome/ODP_Space/Manuscript/dataForAnalysis/alphafold3/fold_pg_dsc1/fold_pg_dsc1_model_0.cif
Chain information for fold_pg_dsc1_model_0.cif #1
---
Chain | Description
A | .
B | .
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (chain colors)"
Using preset: Initial Styles / Space-Filling (Chain Colors)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (single color)"
Using preset: Initial Styles / Space-Filling (Single Color)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> 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" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 7096 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "molecular surfaces" "chain id coloring (opaque)"
Using preset: Molecular Surfaces / Chain ID Coloring (Opaque)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> color bfactor
7096 atoms, 924 residues, 2 surfaces, atom bfactor range 13.2 to 98.8
> color bychain
> select /B & @@bfactor>=70
415 atoms, 422 bonds, 61 residues, 1 model selected
> open
> /Users/shruthi/Library/CloudStorage/Dropbox/Desmosome/ODP_Space/Manuscript/dataForAnalysis/alphafold3/fold_pg_dsc1/pg-
> dsc1-pg-dsc1_modified.pdb
Chain information for pg-dsc1-pg-dsc1_modified.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> select /A & @@bfactor>=70
6060 atoms, 6032 bonds, 799 residues, 2 models selected
> select @@bfactor>=70
9364 atoms, 9266 bonds, 1204 residues, 2 models selected
> select #1 & @@bfactor>=70
4472 atoms, 4532 bonds, 623 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> name frozen "select #1 & @@bfactor>=70" sel
Not registering illegal selector name "select #1 & @@bfactor>=70"
> name frozen "select #1 & @@bfactor>=70" sel
Not registering illegal selector name "select #1 & @@bfactor>=70"
> ui tool show "Selection Inspector"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save
> /Users/shruthi/Library/CloudStorage/Dropbox/Desmosome/ODP_Space/Manuscript/dataForAnalysis/alphafold3/fold_pg_dsc1/af3_pg_dsc1_plddt70.pdb
> models #1 selectedOnly true
> select #2:/A,/C
Expected an objects specifier or a keyword
> select #2:/A,C
Expected an objects specifier or a keyword
> select #2:/A,/C
Expected an objects specifier or a keyword
> select #2:.A,.C
Expected an objects specifier or a keyword
> select #2:/D,G
Expected an objects specifier or a keyword
> select #2:/A,C
Expected an objects specifier or a keyword
> select #2:/A,/C
Expected an objects specifier or a keyword
> select #2
9197 atoms, 9330 bonds, 1198 residues, 1 model selected
> select #2/A,C
4660 atoms, 4728 bonds, 607 residues, 1 model selected
> save
> /Users/shruthi/Library/CloudStorage/Dropbox/Desmosome/ODP_Space/Manuscript/dataForAnalysis/alphafold3/fold_pg_dsc1/homo_pg_dsc1_AC.pdb
> models #2 selectedOnly true
> open
> /Users/shruthi/Library/CloudStorage/Dropbox/Desmosome/ODP_Space/Manuscript/dataForAnalysis/alphafold3/fold_pg_dsc1/homo_pg_dsc1_AC.pdb
Summary of feedback from opening
/Users/shruthi/Library/CloudStorage/Dropbox/Desmosome/ODP_Space/Manuscript/dataForAnalysis/alphafold3/fold_pg_dsc1/homo_pg_dsc1_AC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 56 56 ILE B 127 ILE B 131 1 5
Start residue of secondary structure not found: HELIX 57 57 TYR B 133 LEU B
144 1 12
Start residue of secondary structure not found: HELIX 58 58 PRO B 145 ASN B
152 1 8
Start residue of secondary structure not found: HELIX 59 59 PRO B 156 GLN B
168 1 13
Start residue of secondary structure not found: HELIX 60 60 LEU B 169 LYS B
171 1 3
49 messages similar to the above omitted
Chain information for homo_pg_dsc1_AC.pdb #3
---
Chain | Description
A | No description available
C | No description available
> open
> /Users/shruthi/Library/CloudStorage/Dropbox/Desmosome/ODP_Space/Manuscript/dataForAnalysis/alphafold3/fold_pg_dsc1/af3_pg_dsc1_plddt70.pdb
Summary of feedback from opening
/Users/shruthi/Library/CloudStorage/Dropbox/Desmosome/ODP_Space/Manuscript/dataForAnalysis/alphafold3/fold_pg_dsc1/af3_pg_dsc1_plddt70.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER A 77 ALA A 82 1 6
Start residue of secondary structure not found: HELIX 2 2 ASN A 112 ASN A 132
1 21
Start residue of secondary structure not found: HELIX 55 55 ILE B 13 ASN B 17
1 5
Start residue of secondary structure not found: HELIX 56 56 GLU B 32 ASN B 34
1 3
Start residue of secondary structure not found: HELIX 57 57 THR B 96 LYS B 126
1 31
Chain information for af3_pg_dsc1_plddt70.pdb #4
---
Chain | Description
A | No description available
B | No description available
> select add #1
11756 atoms, 11942 bonds, 1531 residues, 2 models selected
> select add #2
16293 atoms, 16544 bonds, 2122 residues, 4 models selected
> select down
16293 atoms, 16544 bonds, 2122 residues, 4 models selected
> close #1
> close #2
> hide #3 models
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> color #!4 bychain
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> open
> /Users/shruthi/Library/CloudStorage/Dropbox/Desmosome/ODP_Space/Manuscript/dataForAnalysis/alphafold3/fold_pg_dsc1/homo_pg_dsc1_AC.pdb
Summary of feedback from opening
/Users/shruthi/Library/CloudStorage/Dropbox/Desmosome/ODP_Space/Manuscript/dataForAnalysis/alphafold3/fold_pg_dsc1/homo_pg_dsc1_AC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 56 56 ILE B 127 ILE B 131 1 5
Start residue of secondary structure not found: HELIX 57 57 TYR B 133 LEU B
144 1 12
Start residue of secondary structure not found: HELIX 58 58 PRO B 145 ASN B
152 1 8
Start residue of secondary structure not found: HELIX 59 59 PRO B 156 GLN B
168 1 13
Start residue of secondary structure not found: HELIX 60 60 LEU B 169 LYS B
171 1 3
49 messages similar to the above omitted
Chain information for homo_pg_dsc1_AC.pdb #1
---
Chain | Description
A | No description available
C | No description available
> select add #3
4660 atoms, 4728 bonds, 607 residues, 1 model selected
> close #3
> hide #!4 models
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> color #!1 bychain
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #4/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
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 homo_pg_dsc1_AC.pdb, chain A (#1) with af3_pg_dsc1_plddt70.pdb,
chain A (#4), sequence alignment score = 2728.8
RMSD between 497 pruned atom pairs is 0.892 angstroms; (across all 535 pairs:
2.155)
> show #!4 models
> set bgColor white
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset "initial styles" "space-filling (chain colors)"
Using preset: Initial Styles / Space-Filling (Chain Colors)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (single color)"
Using preset: Initial Styles / Space-Filling (Single Color)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> 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 "molecular surfaces" "chain id coloring (opaque)"
Using preset: Molecular Surfaces / Chain ID Coloring (Opaque)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> help help:user/preferences.html#startup
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Basic Actions"
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> color bfactor
9132 atoms, 1230 residues, 4 surfaces, atom bfactor range 15.8 to 291
> ui tool show "Side View"
> view
> view orient
> set bgColor gray
> set bgColor white
> set bgColor black
> graphics silhouettes true
> 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 "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> 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 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> color bypolymer
> color bychain
> rainbow
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
af3_pg_dsc1_plddt70.pdb #4/A PRO 119
af3_pg_dsc1_plddt70.pdb #4/A SER 120
af3_pg_dsc1_plddt70.pdb #4/A GLN 121
af3_pg_dsc1_plddt70.pdb #4/A LEU 122
af3_pg_dsc1_plddt70.pdb #4/A LYS 124
af3_pg_dsc1_plddt70.pdb #4/A SER 125
af3_pg_dsc1_plddt70.pdb #4/A HIS 129
af3_pg_dsc1_plddt70.pdb #4/A ASN 132
af3_pg_dsc1_plddt70.pdb #4/A ALA 137
af3_pg_dsc1_plddt70.pdb #4/A GLU 138
af3_pg_dsc1_plddt70.pdb #4/A LEU 139
af3_pg_dsc1_plddt70.pdb #4/A ARG 142
af3_pg_dsc1_plddt70.pdb #4/A LYS 149
af3_pg_dsc1_plddt70.pdb #4/A GLU 154
af3_pg_dsc1_plddt70.pdb #4/A LYS 172
af3_pg_dsc1_plddt70.pdb #4/A GLU 173
af3_pg_dsc1_plddt70.pdb #4/A ARG 177
af3_pg_dsc1_plddt70.pdb #4/A GLN 184
af3_pg_dsc1_plddt70.pdb #4/A ARG 191
af3_pg_dsc1_plddt70.pdb #4/A ARG 203
af3_pg_dsc1_plddt70.pdb #4/A ARG 216
af3_pg_dsc1_plddt70.pdb #4/A GLU 217
af3_pg_dsc1_plddt70.pdb #4/A LYS 224
af3_pg_dsc1_plddt70.pdb #4/A ARG 233
af3_pg_dsc1_plddt70.pdb #4/A GLU 240
af3_pg_dsc1_plddt70.pdb #4/A GLU 258
af3_pg_dsc1_plddt70.pdb #4/A MET 262
af3_pg_dsc1_plddt70.pdb #4/A LYS 272
af3_pg_dsc1_plddt70.pdb #4/A LYS 283
af3_pg_dsc1_plddt70.pdb #4/A GLN 300
af3_pg_dsc1_plddt70.pdb #4/A GLN 313
af3_pg_dsc1_plddt70.pdb #4/A GLN 317
af3_pg_dsc1_plddt70.pdb #4/A ARG 320
af3_pg_dsc1_plddt70.pdb #4/A LYS 326
af3_pg_dsc1_plddt70.pdb #4/A ARG 333
af3_pg_dsc1_plddt70.pdb #4/A GLU 350
af3_pg_dsc1_plddt70.pdb #4/A LYS 359
af3_pg_dsc1_plddt70.pdb #4/A LYS 385
af3_pg_dsc1_plddt70.pdb #4/A LYS 424
af3_pg_dsc1_plddt70.pdb #4/A ASP 447
af3_pg_dsc1_plddt70.pdb #4/A LYS 448
af3_pg_dsc1_plddt70.pdb #4/A ASP 449
af3_pg_dsc1_plddt70.pdb #4/A ARG 465
af3_pg_dsc1_plddt70.pdb #4/A MET 471
af3_pg_dsc1_plddt70.pdb #4/A LYS 487
af3_pg_dsc1_plddt70.pdb #4/A GLN 491
af3_pg_dsc1_plddt70.pdb #4/A PRO 492
af3_pg_dsc1_plddt70.pdb #4/A ASN 493
af3_pg_dsc1_plddt70.pdb #4/A GLN 494
af3_pg_dsc1_plddt70.pdb #4/A GLN 519
af3_pg_dsc1_plddt70.pdb #4/A ARG 526
af3_pg_dsc1_plddt70.pdb #4/A LYS 533
af3_pg_dsc1_plddt70.pdb #4/A GLN 539
af3_pg_dsc1_plddt70.pdb #4/A ARG 540
af3_pg_dsc1_plddt70.pdb #4/A HIS 541
af3_pg_dsc1_plddt70.pdb #4/A THR 546
af3_pg_dsc1_plddt70.pdb #4/A THR 551
af3_pg_dsc1_plddt70.pdb #4/A ASP 552
af3_pg_dsc1_plddt70.pdb #4/A ARG 555
af3_pg_dsc1_plddt70.pdb #4/A MET 575
af3_pg_dsc1_plddt70.pdb #4/A MET 578
af3_pg_dsc1_plddt70.pdb #4/A ARG 582
af3_pg_dsc1_plddt70.pdb #4/A GLN 591
af3_pg_dsc1_plddt70.pdb #4/A GLU 598
af3_pg_dsc1_plddt70.pdb #4/A ARG 602
af3_pg_dsc1_plddt70.pdb #4/A LYS 615
af3_pg_dsc1_plddt70.pdb #4/A GLU 616
af3_pg_dsc1_plddt70.pdb #4/A MET 631
af3_pg_dsc1_plddt70.pdb #4/A GLU 632
af3_pg_dsc1_plddt70.pdb #4/A ARG 637
af3_pg_dsc1_plddt70.pdb #4/A GLU 639
af3_pg_dsc1_plddt70.pdb #4/A ARG 651
af3_pg_dsc1_plddt70.pdb #4/A GLU 654
af3_pg_dsc1_plddt70.pdb #4/A ASP 655
af3_pg_dsc1_plddt70.pdb #4/A LYS 656
af3_pg_dsc1_plddt70.pdb #4/A ASN 657
af3_pg_dsc1_plddt70.pdb #4/A ASP 659
af3_pg_dsc1_plddt70.pdb #4/A TYR 660
af3_pg_dsc1_plddt70.pdb #4/A ARG 661
af3_pg_dsc1_plddt70.pdb #4/A LYS 662
af3_pg_dsc1_plddt70.pdb #4/A ARG 663
af3_pg_dsc1_plddt70.pdb #4/A GLU 667
af3_pg_dsc1_plddt70.pdb #4/A LEU 672
af3_pg_dsc1_plddt70.pdb #4/A LYS 674
af3_pg_dsc1_plddt70.pdb #4/A HIS 675
af3_pg_dsc1_plddt70.pdb #4/A ASP 676
af3_pg_dsc1_plddt70.pdb #4/A TRP 680
af3_pg_dsc1_plddt70.pdb #4/A GLU 681
af3_pg_dsc1_plddt70.pdb #4/A GLN 684
af3_pg_dsc1_plddt70.pdb #4/A SER 685
af3_pg_dsc1_plddt70.pdb #4/A MET 686
af3_pg_dsc1_plddt70.pdb #4/A ILE 687
af3_pg_dsc1_plddt70.pdb #4/A PRO 688
af3_pg_dsc1_plddt70.pdb #4/B ILE 19
af3_pg_dsc1_plddt70.pdb #4/B ALA 100
af3_pg_dsc1_plddt70.pdb #4/B TYR 101
af3_pg_dsc1_plddt70.pdb #4/B THR 102
af3_pg_dsc1_plddt70.pdb #4/B ASP 103
af3_pg_dsc1_plddt70.pdb #4/B GLN 105
af3_pg_dsc1_plddt70.pdb #4/B GLN 109
af3_pg_dsc1_plddt70.pdb #4/B ARG 111
af3_pg_dsc1_plddt70.pdb #4/B GLU 114
af3_pg_dsc1_plddt70.pdb #4/B LYS 115
af3_pg_dsc1_plddt70.pdb #4/B GLN 121
af3_pg_dsc1_plddt70.pdb #4/B ASP 122
af3_pg_dsc1_plddt70.pdb #4/B GLU 123
af3_pg_dsc1_plddt70.pdb #4/B GLU 124
af3_pg_dsc1_plddt70.pdb #4/B CYS 128
af3_pg_dsc1_plddt70.pdb #4/B GLU 129
af3_pg_dsc1_plddt70.pdb #4/B LYS 140
af3_pg_dsc1_plddt70.pdb #4/B GLY 158
af3_pg_dsc1_plddt70.pdb #4/B LEU 159
af3_pg_dsc1_plddt70.pdb #4/B GLU 160
af3_pg_dsc1_plddt70.pdb #4/B HIS 164
af3_pg_dsc1_plddt70.pdb #4/B GLU 166
af3_pg_dsc1_plddt70.pdb #4/B ARG 170
af3_pg_dsc1_plddt70.pdb #4/B LYS 174
af3_pg_dsc1_plddt70.pdb #4/B THR 175
af3_pg_dsc1_plddt70.pdb #4/B CYS 176
af3_pg_dsc1_plddt70.pdb #4/B ILE 177
af3_pg_dsc1_plddt70.pdb #4/B LYS 178
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for af3_pg_dsc1_plddt70.pdb_A SES surface #4.2: minimum,
-21.29, mean -0.32, maximum 19.66
Coulombic values for af3_pg_dsc1_plddt70.pdb_B SES surface #4.3: minimum,
-10.17, mean 0.69, maximum 10.03
Coulombic values for homo_pg_dsc1_AC.pdb_A SES surface #1.1: minimum, -21.42,
mean -0.25, maximum 14.43
Coulombic values for homo_pg_dsc1_AC.pdb_C SES surface #1.2: minimum, -17.47,
mean -2.69, maximum 9.79
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp
Map values for surface "af3_pg_dsc1_plddt70.pdb_A SES surface": minimum -29.2,
mean -3.616, maximum 25.63
Map values for surface "af3_pg_dsc1_plddt70.pdb_B SES surface": minimum
-26.31, mean -2.301, maximum 22.57
Map values for surface "homo_pg_dsc1_AC.pdb_A SES surface": minimum -29.76,
mean -4.288, maximum 24.26
Map values for surface "homo_pg_dsc1_AC.pdb_C SES surface": minimum -27.8,
mean -5.594, maximum 24.95
To also show corresponding color key, enter the above mlp command and add key
true
> color bfactor
9132 atoms, 1230 residues, 4 surfaces, atom bfactor range 15.8 to 291
> color bynucleotide
> color bypolymer
> color bychain
> color bypolymer
> color bychain
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> select #1/A#4/A
8236 atoms, 8349 bonds, 3 pseudobonds, 1108 residues, 3 models selected
> 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
> show sel cartoons
> hide sel atoms
> select clear
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> style ball
Changed 9132 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style sphere
Changed 9132 atom styles
> style stick
Changed 9132 atom styles
> show atoms
> style sphere
Changed 9132 atom styles
> style ball
Changed 9132 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style stick
Changed 9132 atom styles
> hide atoms
> hide surfaces
> show surfaces
> hide cartoons
> hide surfaces
> hide cartoons
> show cartoons
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> preset "molecular surfaces" "chain id coloring (opaque)"
Using preset: Molecular Surfaces / Chain ID Coloring (Opaque)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> 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
> hide surfaces
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> hide surfaces
> hide atoms
> show cartoons
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> 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
> color bychain
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> rmsd #1/B@CA #2/C@CA
Missing required "to" argument
> rmsd #1/B@CA #2/C@CA
Missing required "to" argument
> rmsd #1/B@CA to #2/C@CA
Given atom specs don't contain any atoms
> rmsd #2/B@CA to #1/C@CA
Number of atoms from first atom spec (0) differs from number in second (61)
> open
> /Users/shruthi/Library/CloudStorage/Dropbox/Desmosome/ODP_Space/Manuscript/dataForAnalysis/alphafold3/fold_pg_dsc1/af3_pg_dsc1_plddt70.pdb
Summary of feedback from opening
/Users/shruthi/Library/CloudStorage/Dropbox/Desmosome/ODP_Space/Manuscript/dataForAnalysis/alphafold3/fold_pg_dsc1/af3_pg_dsc1_plddt70.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER A 77 ALA A 82 1 6
Start residue of secondary structure not found: HELIX 2 2 ASN A 112 ASN A 132
1 21
Start residue of secondary structure not found: HELIX 55 55 ILE B 13 ASN B 17
1 5
Start residue of secondary structure not found: HELIX 56 56 GLU B 32 ASN B 34
1 3
Start residue of secondary structure not found: HELIX 57 57 THR B 96 LYS B 126
1 31
Chain information for af3_pg_dsc1_plddt70.pdb #2
---
Chain | Description
A | No description available
B | No description available
> select add #4
4472 atoms, 4532 bonds, 6 pseudobonds, 623 residues, 2 models selected
> open
> /Users/shruthi/Library/CloudStorage/Dropbox/Desmosome/ODP_Space/Manuscript/dataForAnalysis/alphafold3/fold_pg_dsc1/fold_pg_dsc1_model_0.cif
Chain information for fold_pg_dsc1_model_0.cif #3
---
Chain | Description
A | .
B | .
> close #2
> close #4
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8rc202406060152 (2024-06-06)
© 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 M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: Z15T000JTHN/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 26 days, 3 hours, 33 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
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Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
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EB321HQU C:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
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
ChimeraX-AtomicLibrary: 14.0.5
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: 1.8rc202406060152
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: 1.5.16
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: 3.0.46
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
traitlets: 5.14.2
typing-extensions: 4.12.1
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 , 16 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash waking Mac up from sleep |
comment:2 by , 16 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
ChimeraX crashed due to a bug in the Qt window toolkit. The crash can happen when plugging in or unplugging an external display or when waking from sleep with an external display. It only happens on Mac. It may be fixed in the ChimeraX daily build which uses Qt version 6.7. The ChimeraX 1.8 release uses Qt 6.6 which has the bug. We don't have a way to fix this, it is up to the Qt window toolkit developers to fix it. Report the crash again if you see it in the ChimeraX daily build.
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Reported by Shruthi