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Opened 7 months ago
Closed 7 months ago
#17110 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-15.3.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x000000020343c840 (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.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.chem_group._chem_group, PIL._imagingmath, chimerax.atom_search.ast, chimerax.coulombic._esp, chimerax.mlp._mlp, cython.cimports.libc.math, 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._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._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct (total: 114)
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"uptime" : 220000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 3275,
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"build" : "24D70",
"releaseType" : "User"
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"captureTime" : "2025-03-17 08:27:05.1897 -0600",
"codeSigningMonitor" : 1,
"incident" : "2102D4B6-3180-4355-96BF-6B4D758CB7E6",
"pid" : 84578,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-16 16:43:36.6588 -0600",
"procStartAbsTime" : 4956886680671,
"procExitAbsTime" : 5348198696002,
"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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"crashReporterKey" : "80E5079A-C780-0719-248C-0731A046284A",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"wakeTime" : 8,
"sleepWakeUUID" : "160C7FEC-D6BB-4D7B-9F04-CCCDAAD6B7CF",
"sip" : "enabled",
"vmRegionInfo" : "0x1e82d7a53658 is not in any region. Bytes after previous region: 33066276173401 Bytes before following region: 72005803755944\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, 0x00009e82d7a53658","rawCodes":[1,174284800865880],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00009e82d7a53658 -> 0x00001e82d7a53658 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":84578},
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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/dsimberg/Downloads/fold_2025_03_10_16_50_b3col1/fold_2025_03_10_16_50_b3col1_model_0.cif
> format mmcif
Chain information for fold_2025_03_10_16_50_b3col1_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
> style sphere
Changed 1052 atom styles
> select add #1
1052 atoms, 1079 bonds, 137 residues, 1 model selected
> style sel sphere
Changed 1052 atom styles
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 1052 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> 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 "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> view sel
> show (#!1 & sel) target ab
> ui tool show Toolbar
> set bgColor white
> style sel sphere
Changed 1052 atom styles
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> style sel sphere
Changed 1052 atom styles
> style sel stick
Changed 1052 atom styles
> hide sel atoms
> show sel atoms
> lighting simple
> lighting soft
> lighting full
> cartoon (#!1 & sel)
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> cartoon (#!1 & sel)
> select hydroxyl
35 atoms, 35 residues, 1 model selected
> show (#!1 & sel-residues & sidechain) target ab
> style sel sphere
Changed 35 atom styles
> style sel ball
Changed 35 atom styles
> style sel sphere
Changed 35 atom styles
> style sel sphere
Changed 35 atom styles
> style sel stick
Changed 35 atom styles
> surface (#!1 & sel)
> surface hidePatches (#!1 & sel)
> style (#!1 & sel) sphere
Changed 35 atom styles
> style (#!1 & sel) ball
Changed 35 atom styles
> style (#!1 & sel) stick
Changed 35 atom styles
> select add #1
1052 atoms, 1079 bonds, 137 residues, 2 models selected
> style sel sphere
Changed 1052 atom styles
> select
1052 atoms, 1079 bonds, 137 residues, 1 model selected
> style sel sphere
Changed 1052 atom styles
> style sel sphere
Changed 1052 atom styles
> style sel sphere
Changed 1052 atom styles
> style sel ball
Changed 1052 atom styles
> style sel sphere
Changed 1052 atom styles
> show (#!1 & sel-residues & sidechain) target ab
> select subtract #1
1 model selected
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dsimberg/Desktop/movie1.mp4
Movie saved to /Users/dsimberg/Desktop/movie1.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dsimberg/Desktop/movie2.mp4
Movie saved to /Users/dsimberg/Desktop/movie2.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dsimberg/Desktop/movie3.mp4
Movie saved to /Users/dsimberg/Desktop/movie3.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dsimberg/Desktop/movie4.mp4
Movie saved to /Users/dsimberg/Desktop/movie4.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dsimberg/Desktop/movie5.mp4
Movie saved to /Users/dsimberg/Desktop/movie5.mp4
> save /Users/dsimberg/Desktop/rotatte.gif width 882 height 739 supersample 3
> show target ab
> style stick
Changed 1052 atom styles
> save /Users/dsimberg/Desktop/image9.png supersample 3
> save /Users/dsimberg/Desktop/image10.png supersample 3
> color byhetero
> color bychain
> color byhetero
> color bypolymer
> rainbow
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_2025_03_10_16_50_b3col1_model_0.cif_A SES surface
#1.1: minimum, -16.85, mean -0.59, maximum 12.94
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic
Coulombic values for fold_2025_03_10_16_50_b3col1_model_0.cif_A SES surface
#1.1: minimum, -16.85, mean -0.59, maximum 12.94
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp
Map values for surface "fold_2025_03_10_16_50_b3col1_model_0.cif_A SES
surface": minimum -27.02, mean -5.279, maximum 22.97
To also show corresponding color key, enter the above mlp command and add key
true
> color bfactor
1052 atoms, 137 residues, 1 surfaces, atom bfactor range 26.3 to 98.9
> hbonds reveal true
109 hydrogen bonds found
> hbonds reveal true
109 hydrogen bonds found
> ~hbonds
> hbonds reveal true
109 hydrogen bonds found
> interfaces ~solvent
0 buried areas:
> interfaces ~solvent
0 buried areas:
> color byhetero
> color bychain
> color bypolymer
> rainbow
> style stick
Changed 1052 atom styles
> style stick
Changed 1052 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> hide #1.2 models
> hide #1.1 models
> style stick
Changed 1052 atom styles
> style sphere
Changed 1052 atom styles
> color bychain
> color byhetero
> coulombic
Coulombic values for fold_2025_03_10_16_50_b3col1_model_0.cif_A SES surface
#1.1: minimum, -16.85, mean -0.59, maximum 12.94
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!1 models
> show #!1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> style stick
Changed 1052 atom styles
> hide surfaces
> color #1 #e4e5ebff
> color #1 #bdbec4ff
> color #1 #737478ff
> color #1 #828286ff
> show cartoons
> show atoms
> select add #1.1
1052 atoms, 137 residues, 1 model selected
> select subtract #1.1
1 model selected
> hide atoms
> hide cartoons
> show cartoons
> show surfaces
> style stick
Changed 1052 atom styles
> style stick
Changed 1052 atom styles
> hide surfaces
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> 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 byhetero
> show atoms
> hide atoms
> show cartoons
> hide cartoons
> show cartoons
> transparency 0
> volume showOutlineBox true
No volumes specified
> transparency 50
> transparency 0
> transparency 50
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
> volume style surface
No volumes specified
> volume style surface
No volumes specified
> volume hide
No volumes specified
> volume hide
No volumes specified
> lighting shadows false
> lighting simple
> lighting full
> lighting soft
> set bgColor gray
> set bgColor white
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
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
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
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 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 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
> 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
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:99
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:99-118
154 atoms, 159 bonds, 7 pseudobonds, 20 residues, 2 models selected
> color (#!1 & sel) purple
> select /A:48
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:48-62
108 atoms, 109 bonds, 6 pseudobonds, 15 residues, 2 models selected
> color (#!1 & sel) red
> select /A:28
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:28-36
71 atoms, 73 bonds, 2 pseudobonds, 9 residues, 2 models selected
> color (#!1 & sel) blue
> select add #1
1052 atoms, 1079 bonds, 109 pseudobonds, 137 residues, 3 models selected
> select subtract #1
1 model selected
> hide #!1 models
> show #!1 models
> select add #1
1052 atoms, 1079 bonds, 109 pseudobonds, 137 residues, 2 models selected
> select /A:28
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:28-36
71 atoms, 73 bonds, 2 pseudobonds, 9 residues, 2 models selected
> select add #1
1052 atoms, 1079 bonds, 109 pseudobonds, 137 residues, 3 models selected
> select subtract #1.1
1 model selected
> ui tool show "Side View"
> graphics silhouettes false
> graphics silhouettes true
> view
> view orient
> view
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select add #1
1052 atoms, 1079 bonds, 109 pseudobonds, 137 residues, 2 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
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> graphics silhouettes false
> graphics silhouettes true
> select hydroxyl
35 atoms, 35 residues, 1 model selected
> show sel atoms
> show (#!1 & sel-residues & sidechain) target ab
> color sel byhetero
> select add #1
1052 atoms, 1079 bonds, 109 pseudobonds, 137 residues, 3 models selected
> color sel byhetero
> coulombic sel
Coulombic values for fold_2025_03_10_16_50_b3col1_model_0.cif_A SES surface
#1.1: minimum, -16.85, mean -0.59, maximum 12.94
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel byhetero
> style sel sphere
Changed 1052 atom styles
> style sel ball
Changed 1052 atom styles
> style sel stick
Changed 1052 atom styles
> hide sel surfaces
> show sel cartoons
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> 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" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> show sel atoms
> color sel byhetero
> show sel surfaces
> hide sel surfaces
> hide sel atoms
> select hydroxyl
35 atoms, 35 residues, 1 model selected
> show sel atoms
> show (#!1 & sel-residues & sidechain) target ab
> 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 subtract #1.1
1 model selected
> select add #1.1
1052 atoms, 137 residues, 1 model selected
> select subtract #1.1
1 model selected
> select add #1
1052 atoms, 1079 bonds, 109 pseudobonds, 137 residues, 2 models selected
> select subtract #1
1 model selected
> select add #1
1052 atoms, 1079 bonds, 109 pseudobonds, 137 residues, 2 models selected
> color sel byhetero
> 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
> select subtract #1
1 model selected
> select add #1.1
1052 atoms, 137 residues, 1 model selected
> select subtract #1.1
1 model selected
> select add #1
1052 atoms, 1079 bonds, 109 pseudobonds, 137 residues, 2 models selected
> select subtract #1
1 model selected
> hide cartoons
> hide atoms
> color byhetero
> coulombic
Coulombic values for fold_2025_03_10_16_50_b3col1_model_0.cif_A SES surface
#1.1: minimum, -16.85, mean -0.59, maximum 12.94
To also show corresponding color key, enter the above coulombic command and
add key true
> hide surfaces
> show cartoons
> show atoms
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGQ3LL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 5 days, 23 hours, 41 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Thunderbolt Display:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 7 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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