![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17518 closed defect (duplicate)
Graphics hardware encountered an error and was reset
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.7.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00007ff85f298940 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 556 in swap_buffers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 202 in draw
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 60)
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{
"uptime" : 360000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro14,1",
"coalitionID" : 35177,
"osVersion" : {
"train" : "macOS 13.7.1",
"build" : "22H221",
"releaseType" : "User"
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"captureTime" : "2025-04-30 08:32:13.9356 -0400",
"incident" : "901CBE94-B2B4-4CE4-A310-0927CBA2AD1B",
"pid" : 27853,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-26 09:50:47.0177 -0400",
"procStartAbsTime" : 283761553571052,
"procExitAbsTime" : 368334336402066,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"6EE9740B-A496-5619-B776-963B1C600DE2","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "1BC9ED74-A73A-BB75-8E2C-1774CFA56FB6",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 1947,
"sleepWakeUUID" : "95C5BA37-79F0-4A60-AA79-6C6DF437B33C",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":27853},
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000011\n"],
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"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/olgabednova/Desktop/rat_aNGF_Fab_mNGF_docked.cxs
Log from Fri Apr 4 09:11:39 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/olgabednova/Desktop/rat_aNGF_Fab_mNGF_docked.cxs format session
Log from Thu Mar 6 09:54:59 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/olgabednova/Downloads/model_02.pdb
model_02.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]
Chain information for model_02.pdb #1
---
Chain | Description
A | No description available
B | No description available
Non-standard residues in model_02.pdb #1
---
MG — (MG)
> select /A
1668 atoms, 1707 bonds, 212 residues, 1 model selected
> ui tool show "Renumber Residues"
> renumber /A seqStart 1
0 residues renumbered
> renumber /A seqStart 1
0 residues renumbered
> select ~sel
1648 atoms, 1688 bonds, 219 residues, 1 model selected
> ui tool show "Renumber Residues"
> renumber /B seqStart 213
217 residues renumbered
> renumber /B seqStart 213
0 residues renumbered
> undo
> select /A:1-212
1668 atoms, 1707 bonds, 212 residues, 1 model selected
> select /A:1-212
1668 atoms, 1707 bonds, 212 residues, 1 model selected
> select /B:1-217
42 atoms, 41 bonds, 5 residues, 1 model selected
> select /B:1-217
42 atoms, 41 bonds, 5 residues, 1 model selected
> select /A:1-212
1668 atoms, 1707 bonds, 212 residues, 1 model selected
> select /B:1-217
42 atoms, 41 bonds, 5 residues, 1 model selected
> select ~sel
3274 atoms, 3353 bonds, 426 residues, 1 model selected
> select /A
1668 atoms, 1707 bonds, 212 residues, 1 model selected
> select /B
1646 atoms, 1688 bonds, 217 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel A
Chain IDs of 217 residues changed
> changechains sel A
Chain IDs of 0 residues changed
> select /A
3314 atoms, 3395 bonds, 429 residues, 1 model selected
> select /B
Nothing selected
> select /A
3314 atoms, 3395 bonds, 429 residues, 1 model selected
> ui tool show "Dock Prep"
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Summary of feedback from adding hydrogens to model_02.pdb #1
---
notes | No usable SEQRES records for model_02.pdb (#1) chain A; guessing termini instead
No usable SEQRES records for model_02.pdb (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A ASP 1, /A GLN 213
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A ASN 212, /A CYS 429
Chain-final residues that are not actual C termini:
384 hydrogen bonds
3250 hydrogens added
Closest equivalent command: addcharge standardizeResidues none
Using Amber 20 recommended default charges and atom types for standard
residues
Dock prep finished
> save /Users/olgabednova/Desktop/rat_aNGF_Fab_prepared.pdb relModel #1
> open
> /Users/olgabednova/Downloads/453316-rat_aNGF_mNGF_summary-2/cluster1_1.pdb
Summary of feedback from opening
/Users/olgabednova/Downloads/453316-rat_aNGF_mNGF_summary-2/cluster1_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_45w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_45.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Chain information for cluster1_1.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide #1 models
> ui mousemode right zoom
> ui mousemode right translate
> select #2/B
2155 atoms, 2188 bonds, 1 pseudobond, 220 residues, 2 models selected
> color pink
> undo
> ui tool show H-Bonds
> hbonds twoColors true saltOnly true reveal true
54 hydrogen bonds found
31 strict hydrogen bonds found
> hbonds twoColors true saltOnly true reveal true
54 hydrogen bonds found
31 strict hydrogen bonds found
> ui tool show ViewDockX
No suitable models found for ViewDockX
> ui tool show Contacts
> contacts resSeparation 5 ignoreHiddenModels true
3745 contacts
> contacts resSeparation 5 ignoreHiddenModels true
3745 contacts
> undo
> hide
> undo
> hide #4 models
> ui mousemode right zoom
> surface #2-3
> select #2/A
4075 atoms, 4156 bonds, 2446 pseudobonds, 429 residues, 4 models selected
> color (#!2 & sel) orange
> hide (#!2 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!2 & sel-residues)
> show (#!2 & sel-residues & backbone) target ab
> select #2/B
2155 atoms, 2188 bonds, 1102 pseudobonds, 220 residues, 4 models selected
> surface hidePatches (#!2 & sel)
> volume style mesh
No volumes specified
> volume style surface
No volumes specified
> volume hide
No volumes specified
> hide sel surfaces
> show sel cartoons
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> color sel bychain
[Repeated 1 time(s)]
> undo
[Repeated 1 time(s)]
> mlp sel
Map values for surface "cluster1_1.pdb_B SES surface": minimum -26.86, mean
-4.94, maximum 24.1
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "cluster1_1.pdb_B SES surface": minimum -26.86, mean
-4.94, maximum 24.1
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for cluster1_1.pdb_B SES surface #2.3: minimum, -9.76, mean
1.40, maximum 13.12
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for cluster1_1.pdb_B SES surface #2.3: minimum, -9.76, mean
1.39, maximum 13.12
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for cluster1_1.pdb_B SES surface #2.3: minimum, -9.76, mean
1.39, maximum 13.12
To also show corresponding color key, enter the above coulombic command and
add key true
> 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 "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 12791 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> hide sel atoms
> select #2/B
2152 atoms, 2185 bonds, 1102 pseudobonds, 220 residues, 4 models selected
> hide sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> hide sel surfaces
[Repeated 1 time(s)]
> show sel surfaces
> select #1/A#1/A#2/A
10639 atoms, 10801 bonds, 2458 pseudobonds, 858 residues, 5 models selected
> hide sel & #!2 atoms
> style sel & #!2 sphere
Changed 4075 atom styles
> style sel & #!2 sphere
Changed 4075 atom styles
> show sel & #!2 surfaces
> show sel & #!2 cartoons
[Repeated 1 time(s)]
> hide sel & #!2 cartoons
> interfaces select & #!2 & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & #!2 & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select #2/B
2152 atoms, 2185 bonds, 1102 pseudobonds, 220 residues, 4 models selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> color sel byhetero
> coulombic sel
Coulombic values for cluster1_1.pdb_B SES surface #2.3: minimum, -9.76, mean
1.39, maximum 13.12
To also show corresponding color key, enter the above coulombic command and
add key true
> select #1/A#1/A#2/A
10639 atoms, 10801 bonds, 2458 pseudobonds, 858 residues, 5 models selected
> mlp sel & #!2
Map values for surface "cluster1_1.pdb_A SES surface": minimum -30.04, mean
-6.604, maximum 23.23
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel & #!2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for cluster1_1.pdb_A SES surface #2.2: minimum, -9.77, mean
1.12, maximum 11.63
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel & #!2
Coulombic values for cluster1_1.pdb_A SES surface #2.2: minimum, -9.77, mean
1.12, maximum 11.63
To also show corresponding color key, enter the above coulombic command and
add key true
> hbonds sel & #!2 reveal true
382 hydrogen bonds found
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 4074 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
> hbonds sel & #!2 reveal true
382 hydrogen bonds found
> ui tool show Clashes
> clashes ignoreHiddenModels true
32 clashes
> clashes ignoreHiddenModels true
32 clashes
> show #4 models
> hide #4 models
> color (#!2 & sel) orange red
> deselec
Unknown command: deselec
> deselect
Unknown command: deselect
> cancel selection
Unknown command: cancel selection
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 0 maps.
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
Chains must have same sequence
> select #2/A
4074 atoms, 4155 bonds, 2797 pseudobonds, 429 residues, 5 models selected
Alignment identifier is 2/A
> select #2/A:321-322
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:321-330
83 atoms, 82 bonds, 10 residues, 1 model selected
> hide #5 models
> show #5 models
> hide #3 models
> show #3 models
> hide #5 models
> show #5 models
> hide #3 models
> show #3 models
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select
> #2/A:4-7,10-14,19-25,33-38,45-49,62-67,70-75,84-90,102-107,114-118,129-137,145-150,159-164,174-182,191-197,205-210,215-217,230-237,246-251,258-263,269-271,279-284,289-294,303-309,321-323,334-338,349-359,365-368,377-379,383-385,388-398,408-413,418-423
1913 atoms, 1913 bonds, 1356 pseudobonds, 197 residues, 4 models selected
Drag select of 16 atoms, 3 residues, 15 bonds, 5 pseudobonds
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right translate
> select #2/A:80-82,122-127,183-188,273-275,299-301,369-371
232 atoms, 229 bonds, 10 pseudobonds, 24 residues, 3 models selected
> ui tool show H-Bonds
> hbonds twoColors true slopColor #41f300 saltOnly true reveal true
54 hydrogen bonds found
31 strict hydrogen bonds found
> hbonds twoColors true slopColor #41f300 saltOnly true reveal true
54 hydrogen bonds found
31 strict hydrogen bonds found
> undo
Undo failed, probably because structures have been modified.
> ui tool show H-Bonds
> hbonds distSlop 3.0 twoColors true slopColor #11ed00 saltOnly true reveal
> true
75 hydrogen bonds found
31 strict hydrogen bonds found
> hbonds distSlop 3.0 twoColors true slopColor #11ed00 saltOnly true reveal
> true
75 hydrogen bonds found
31 strict hydrogen bonds found
> select #2/A:213
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:213-214
20 atoms, 19 bonds, 2 residues, 1 model selected
> select #2/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:1-212
2058 atoms, 2097 bonds, 1228 pseudobonds, 212 residues, 4 models selected
> ui tool show "Model Loops"
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select #2/A:80-82,122-127,183-188,273-275,299-301,369-371
232 atoms, 229 bonds, 3 pseudobonds, 24 residues, 3 models selected
> select #2/A:213
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:213-429
2016 atoms, 2058 bonds, 1093 pseudobonds, 217 residues, 4 models selected
> ui tool show "Change Chain IDs"
> ui tool show "Renumber Residues"
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select #2/B
2152 atoms, 2185 bonds, 1125 pseudobonds, 220 residues, 5 models selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select #1/A#1/A#2/A
10638 atoms, 10800 bonds, 2483 pseudobonds, 858 residues, 6 models selected
> ui mousemode right zoom
> hide #5 models
> select add #5
10638 atoms, 10800 bonds, 2503 pseudobonds, 858 residues, 8 models selected
> select subtract #5
10638 atoms, 10800 bonds, 2471 pseudobonds, 858 residues, 7 models selected
> select add #3
10638 atoms, 10800 bonds, 2497 pseudobonds, 858 residues, 7 models selected
> interfaces select & #!2 & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right zoom
> hide #2.1 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #2.1 models
> hide #2.1 models
> show #5 models
> hide #5 models
> show #4 models
> hide #4 models
> hide #3 models
> show #3 models
> hide #2.3 models
> show #2.3 models
> hide #2.3 models
> show #2.3 models
> hide #2.3 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> select subtract #2.2
6564 atoms, 6645 bonds, 40 pseudobonds, 429 residues, 4 models selected
> interfaces #!2 & ~solvent
1 buried areas: A B 1389
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B
Alignment identifier is 2/B
> toolshed show
Downloading bundle ChimeraX_ISOLDE-1.8-cp311-cp311-macosx_10_13_universal2.whl
[Repeated 2 time(s)]
> toolshed show
Downloading bundle ChimeraX_ISOLDE-1.8-cp311-cp311-macosx_10_13_universal2.whl
[Repeated 1 time(s)]
> instal isolde
Unknown command: instal isolde
> install isolde
Unknown command: install isolde
> toolshed install ChimeraX_ISOLDE-1.8-cp311-cp311-macosx_10_13_universal2.whl
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/toolshed.py", line 312, in toolshed_install
ts.install_bundle(bundles, logger, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 931, in install_bundle
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolshed_utils/__init__.py", line 216, in _install_bundle
raise ValueError("Non-existent wheel file")
ValueError: Non-existent wheel file
ValueError: Non-existent wheel file
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolshed_utils/__init__.py", line 216, in _install_bundle
raise ValueError("Non-existent wheel file")
See log for complete Python traceback.
> toolshed install ChimeraX_ISOLDE-1.8-cp311-cp311-macosx_10_13_universal2.whl
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/toolshed.py", line 312, in toolshed_install
ts.install_bundle(bundles, logger, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 931, in install_bundle
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolshed_utils/__init__.py", line 216, in _install_bundle
raise ValueError("Non-existent wheel file")
ValueError: Non-existent wheel file
ValueError: Non-existent wheel file
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolshed_utils/__init__.py", line 216, in _install_bundle
raise ValueError("Non-existent wheel file")
See log for complete Python traceback.
> save /Users/olgabednova/Desktop/rat_aNGF_Fab_mNGF.pdb
> open /Users/olgabednova/Desktop/rat_aNGF_Fab_mNGF.pdb
Summary of feedback from opening
/Users/olgabednova/Desktop/rat_aNGF_Fab_mNGF.pdb
---
warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence records as basis for sequence.
rat_aNGF_Fab_mNGF.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]
Chain information for rat_aNGF_Fab_mNGF.pdb
---
Chain | Description
6.1/A 6.2/A | No description available
6.2/B | No description available
> hide #!2 models
> hide #!6.2 models
> show #!6.2 models
> hide #!6.2 models
> hide #!6.1 models
> show #!6.1 models
> select add #6
13282 atoms, 12983 bonds, 9 pseudobonds, 1121 residues, 8 models selected
> select subtract #6
492 atoms, 43 residues, 3 models selected
> select add #6
13282 atoms, 12983 bonds, 9 pseudobonds, 1121 residues, 8 models selected
> select subtract #6
492 atoms, 43 residues, 3 models selected
> close #6
> show #!2 models
> select subtract #2.3
243 atoms, 21 residues, 3 models selected
> select add #2.3
2395 atoms, 241 residues, 2 models selected
> select subtract #2.3
243 atoms, 21 residues, 3 models selected
> select add #2.3
2395 atoms, 241 residues, 2 models selected
> select subtract #2.3
243 atoms, 21 residues, 3 models selected
> select subtract #2.2
1 model selected
> select add #2.2
4074 atoms, 429 residues, 1 model selected
> select subtract #2.2
1 model selected
> select add #2.2
4074 atoms, 429 residues, 1 model selected
> select subtract #2.2
1 model selected
> show #2.3 models
> select add #2.2
4074 atoms, 429 residues, 1 model selected
> undo
[Repeated 6 time(s)]
> save /Users/olgabednova/Desktop/rat_aNGF_Fab_mNGF_docked.cxs
——— End of log from Thu Mar 6 09:54:59 2025 ———
opened ChimeraX session
> hide all
> show sel target ab
> interfaces select #2/B & ::polymer_type>0 contacting #2/A & ::polymer_type>0
> areaCutoff 0
22 contacting residues
> interfaces select #2/B & ::polymer_type>0 contacting #2/A & ::polymer_type>0
> areaCutoff 0
22 contacting residues
> show (#!2 & sel) target ab
> color (#!2 & sel) lime
> interfaces select #2/A & ::polymer_type>0 contacting #2/B & ::polymer_type>0
> areaCutoff 0
21 contacting residues
> interfaces select #2/A & ::polymer_type>0 contacting #2/B & ::polymer_type>0
> areaCutoff 0
21 contacting residues
> color (#!2 & sel) yellow
> color (#!2 & sel) hot pink
> ui tool show Clashes
> save /Users/olgabednova/Desktop/rat_aNGF_Fab_mNGF_docked.cxs
——— End of log from Fri Apr 4 09:11:39 2025 ———
opened ChimeraX session
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select #2/B
2152 atoms, 2185 bonds, 1125 pseudobonds, 220 residues, 5 models selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select all
12790 atoms, 12985 bonds, 3853 pseudobonds, 1078 residues, 6 models selected
> interfaces select & #!2 & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> deselect
Unknown command: deselect
> cancel
Unknown command: cancel
> stop
> cancel
Unknown command: cancel
> end
Unknown command: end
> interfaces select #1/A & ::polymer_type>0 contacting #2/A & ::polymer_type>0
> areaCutoff 0
37 contacting residues
> interfaces select #1/A & ::polymer_type>0 contacting #2/A & ::polymer_type>0
> areaCutoff 0
37 contacting residues
> show #4 models
> hide #4 models
> interfaces #!2 & ~solvent
1 buried areas: A B 1389
> interfaces select #2/A & ::polymer_type>0 contacting #1/A & ::polymer_type>0
> areaCutoff 0
30 contacting residues
> interfaces select #2/B & ::polymer_type>0 contacting #1/A & ::polymer_type>0
> areaCutoff 0
0 contacting residues
> interfaces select #2/B#2/A & ::polymer_type>0 contacting #1/A#1/A &
> ::polymer_type>0 areaCutoff 0
30 contacting residues
> interfaces select #1/A#1/A & ::polymer_type>0 contacting #2/A#2/B &
> ::polymer_type>0 areaCutoff 0
37 contacting residues
> interfaces select #1/A#1/A & ::polymer_type>0 contacting #2/A#2/B &
> ::polymer_type>0 areaCutoff 0
37 contacting residues
> interfaces select #1/A#1/A & ::polymer_type>0 contacting #2/A#2/B &
> ::polymer_type>0 areaCutoff 0
37 contacting residues
> hide #3 models
> show #3 models
> list contacts
Unknown command: list contacts
> select #2/B
2152 atoms, 2185 bonds, 1125 pseudobonds, 220 residues, 5 models selected
> interfaces select #2/B & ::polymer_type>0 contacting #1/A#1/A &
> ::polymer_type>0 areaCutoff 0
0 contacting residues
> interfaces select #2/B & ::polymer_type>0 contacting #1/A#1/A &
> ::polymer_type>0 areaCutoff 0
0 contacting residues
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #2/A
4074 atoms, 4155 bonds, 2464 pseudobonds, 429 residues, 5 models selected
> interfaces select #2/A & ::polymer_type>0 contacting #2/B & ::polymer_type>0
> areaCutoff 0
21 contacting residues
> interfaces select #2/A & ::polymer_type>0 contacting #2/B & ::polymer_type>0
> areaCutoff 0
21 contacting residues
> list residues
Unknown command: list residues
> list
Unknown command: list
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> ui tool show "Selection Inspector"
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> show #4 models
> hide #4 models
> show #4 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> select add #2
6226 atoms, 6340 bonds, 3834 pseudobonds, 649 residues, 6 models selected
> select subtract #2
2 models selected
> interfaces select #2/B & ::polymer_type>0 contacting #2/A & ::polymer_type>0
> areaCutoff 0
22 contacting residues
> interfaces select #2/B & ::polymer_type>0 contacting #2/A & ::polymer_type>0
> areaCutoff 0
22 contacting residues
> hide #3 models
> show #3 models
> hide #4 models
> show #4 models
> hide #3 models
> show #3 models
> hide #4 models
> show #4 models
> hide #4 models
> color #4 #00efefff models
> show #4 models
> hide #4 target m
> close #4
> interfaces select #2/B & ::polymer_type>0 contacting #2/A & ::polymer_type>0
> areaCutoff 0
22 contacting residues
> interfaces select #2/B & ::polymer_type>0 contacting #2/A & ::polymer_type>0
> areaCutoff 0
22 contacting residues
> show #5 models
> hide #5 models
> interfaces select #2/A & ::polymer_type>0 contacting #2/B & ::polymer_type>0
> areaCutoff 0
21 contacting residues
> interfaces select #2/A & ::polymer_type>0 contacting #2/B & ::polymer_type>0
> areaCutoff 0
21 contacting residues
> interfaces select #2/A & ::polymer_type>0 contacting #2/B & ::polymer_type>0
> areaCutoff 0
21 contacting residues
> interfaces select #2/A & ::polymer_type>0 contacting #2/B & ::polymer_type>0
> areaCutoff 0
21 contacting residues
> interfaces select #2/A & ::polymer_type>0 contacting #2/B & ::polymer_type>0
> areaCutoff 0
21 contacting residues
> myInterfaceResidues
Unknown command: myInterfaceResidues
> toolshed show
> ui mousemode right select
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
> hbonds sel reveal true
33 hydrogen bonds found
> hide #3 models
> show #3 models
> ui mousemode right zoom
> ui mousemode right translate
> hide #!2 models
> hide #3 models
> show #!2 models
> select add #2
6226 atoms, 6340 bonds, 67 pseudobonds, 649 residues, 5 models selected
> select subtract #2
2 models selected
> select ((#2/A & ::polymer_type>0 ) & ((#2/B & ::polymer_type>0 ) :0 ) & ((#2/A & ::polymer_type>0 ) : select ((#2/A & ::polymer_type>0 ) & ((#2/B & ::polymer_type>0 ) :0 ) & ((#2/A & ::polymer_type>0 ) : show #3 models
> hide #3 models
> ui tool show Contacts
> contacts distanceOnly 4.0 intraModel false intraMol false ignoreHiddenModels
> true color #977400
No distances
> ui tool show H-Bonds
> hbonds sel distSlop 3.0 twoColors true slopColor #11ed00 saltOnly true
> reveal true
14 hydrogen bonds found
5 strict hydrogen bonds found
> hbonds sel distSlop 3.0 twoColors true slopColor #11ed00 saltOnly true
> reveal true
14 hydrogen bonds found
5 strict hydrogen bonds found
> show #3 models
> color #3 #00e7e2ff models
> color #3 #0108e7ff models
> color #3 #00d8e3ff models
> select #2/A:309
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/A:309-312
50 atoms, 50 bonds, 2 pseudobonds, 4 residues, 2 models selected
> select
> #2/A:4-7,10-14,19-25,33-38,45-49,62-67,70-75,84-90,102-107,114-118,129-137,145-150,159-164,174-182,191-197,205-210,215-217,230-237,246-251,258-263,269-271,279-284,289-294,303-309,321-323,334-338,349-359,365-368,377-379,383-385,388-398,408-413,418-423
1913 atoms, 1913 bonds, 11 pseudobonds, 197 residues, 2 models selected
> select #2/A:308
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:308-314
71 atoms, 72 bonds, 2 pseudobonds, 7 residues, 2 models selected
> select #2/A:238
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:238-245
86 atoms, 88 bonds, 8 residues, 1 model selected
> select #2/A:308
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:308-316
95 atoms, 97 bonds, 2 pseudobonds, 9 residues, 2 models selected
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.7.3
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.
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 Pro
Model Identifier: MacBookPro14,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 529.140.2.0.0
OS Loader Version: 577.140.2~30
SMC Version (system): 2.43f11
Software:
System Software Overview:
System Version: macOS 13.7.1 (22H221)
Kernel Version: Darwin 22.6.0
Time since boot: 16 days, 28 minutes
Graphics/Displays:
Intel Iris Plus Graphics 640:
Chipset Model: Intel Iris Plus Graphics 640
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5926
Revision ID: 0x0006
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 6 months ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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