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Opened 8 months ago
Closed 8 months ago
#16925 closed defect (duplicate)
Crash in python_instances_of_class
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.4-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403290055 (2024-03-29 00:55:10 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 0x00000001f4a79e00 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 2636 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 256 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 256 in include_state
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 260 in discovery
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 641 in save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 917 in save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95 in save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101 in provider_save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86 in cmd_save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62 in display
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138 in show_save_file_dialog
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/providers.py", line 38 in _file_save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/providers.py", line 56 in run_provider
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/__init__.py", line 37 in run_provider
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 165 in callback
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, lxml._elementpath, lxml.etree, chimerax.surface._surface, chimerax.pdb_lib._load_libs, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, 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.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 59)
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{
"uptime" : 250000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,6",
"coalitionID" : 2359,
"osVersion" : {
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"build" : "22F66",
"releaseType" : "User"
},
"captureTime" : "2025-02-20 17:15:49.1438 -0500",
"incident" : "C3AEA807-63C6-431D-BD7A-A8EAD406F3F9",
"pid" : 58515,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-20 16:44:05.6642 -0500",
"procStartAbsTime" : 6145184084561,
"procExitAbsTime" : 6190867296105,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"97F86206-D27D-5E6E-828E-24510B8A1510","thirdParty":true},
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "374891C2-7817-A0E6-D242-CF314EBC6C71",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 26085,
"sleepWakeUUID" : "578E9156-212E-40E4-9B14-98567E5CD20B",
"sip" : "enabled",
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"exception" : {"codes":"0x0000000000000001, 0x0000000000000158","rawCodes":[1,344],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000158"},
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"faultingThread" : 0,
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"logWritingSignature" : "c8a99de242ad59a5cdafdd423c4bde37abf4c857",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "63582c5f8a53461413999550",
"factorPackIds" : {
},
"deploymentId" : 240000002
},
{
"rolloutId" : "62fe74515312cd4599bd3c80",
"factorPackIds" : {
"MYRIAD_BOOSTS" : "62fe74805312cd4599bd3c81"
},
"deploymentId" : 240000006
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202403290055 (2024-03-29)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/apple/Downloads/6mqt.pdb
6mqt.pdb title:
Hras G12S In complex with GDP [more info...]
Chain information for 6mqt.pdb #1
---
Chain | Description | UniProt
A B C D E F G H | gtpase hras | RASH_HUMAN 1-166
Non-standard residues in 6mqt.pdb #1
---
GDP — guanosine-5'-diphosphate
MG — magnesium ion
997 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #1
22372 atoms, 21505 bonds, 48 pseudobonds, 2375 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B /C /D /E /F /G /H
Alignment identifier is 1
> select /A-H:30-31
216 atoms, 208 bonds, 16 residues, 1 model selected
> select /A-H:30-40
1328 atoms, 1344 bonds, 88 residues, 1 model selected
> color sel magenta
> select /A-H:60
56 atoms, 48 bonds, 8 residues, 1 model selected
> select /A-H:60-76
2112 atoms, 2120 bonds, 136 residues, 1 model selected
> color sel lime
> close #1
> open /Users/apple/Downloads/2quz.pdb
2quz.pdb title:
Crystal structure of the activating H-RASK117R mutant In costello syndrome,
bound to Mg-GDP [more info...]
Chain information for 2quz.pdb #1
---
Chain | Description | UniProt
A | C-H-RAS P21 protein; transforming protein P21; P21RAS; H- RAS-1; C-H-RAS; HA-RAS | RASH_HUMAN 1-166
Non-standard residues in 2quz.pdb #1
---
GDP — guanosine-5'-diphosphate
MG — magnesium ion
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> crystalcontacts #1
5 pairs of asymmetric units of 2quz.pdb contact at distance 3.0 A
Atoms MTRIX SMTRY Unit cell MTRIXref Copies
28 0 16 0 0 0 0 1
11 0 1 0 0 0 0 1
8 0 11 0 0 0 0 1
8 0 9 -1 0 0 0 1
7 0 2 0 0 0 0 1
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:30-31
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:30-40
94 atoms, 96 bonds, 11 residues, 1 model selected
> color sel magenta
> select #1/A:60
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:60-76
141 atoms, 142 bonds, 17 residues, 1 model selected
> color sel lime
> close #1-2
> open /Users/apple/Downloads/7jii.pdb
7jii.pdb title:
Hras A59E GDP [more info...]
Chain information for 7jii.pdb #1
---
Chain | Description | UniProt
A B | gtpase hras | RASH_HUMAN 1-166
Non-standard residues in 7jii.pdb #1
---
CA — calcium ion
GDP — guanosine-5'-diphosphate
MG — magnesium ion
34 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:30-31
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:30-40
85 atoms, 87 bonds, 11 residues, 1 model selected
> color sel magenta
> select /A:60-61
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /A:60-76
137 atoms, 138 bonds, 17 residues, 1 model selected
> color sel lime
> select clear
> crystalcontacts #1
12 pairs of asymmetric units of 7jii.pdb contact at distance 3.0 A
Atoms MTRIX SMTRY Unit cell MTRIXref Copies
18 0 0 -1 0 0 0 1
17 0 0 0 -1 0 0 1
16 0 0 1 0 0 0 1
14 0 0 0 1 0 0 1
10 0 0 -1 -1 -1 0 1
9 0 0 1 1 1 0 1
9 0 0 1 0 1 0 1
8 0 0 -1 0 -1 0 1
4 0 0 0 1 1 0 1
4 0 0 0 0 1 0 1
4 0 0 0 -1 -1 0 1
3 0 0 0 0 -1 0 1
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B
Alignment identifier is 1/B
> select #1/B:30
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:30-40
94 atoms, 96 bonds, 11 residues, 1 model selected
> color sel magenta
> select #1/B:60
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/B:60-76
124 atoms, 124 bonds, 17 residues, 1 model selected
> color sel lime
> select add #1
3005 atoms, 2704 bonds, 29 pseudobonds, 676 residues, 2 models selected
> show sel surfaces
> select #1/A:30
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:30-40
85 atoms, 87 bonds, 11 residues, 1 model selected
> select #1/A:30-40,60-76
222 atoms, 225 bonds, 28 residues, 1 model selected
> select #1/B:30-40,60-76
218 atoms, 220 bonds, 28 residues, 1 model selected
> select #1/B:30-40,60-76
218 atoms, 220 bonds, 28 residues, 1 model selected
> select #1/B:30
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:30-40
94 atoms, 96 bonds, 11 residues, 1 model selected
> select #1/A:30-40,60-76
222 atoms, 225 bonds, 28 residues, 1 model selected
> select #1/A:40
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:30-40
85 atoms, 87 bonds, 11 residues, 1 model selected
> select #1/B:30-40
94 atoms, 96 bonds, 11 residues, 1 model selected
> color (#!1 & sel) magenta
> select #1/A:30
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:30-40
85 atoms, 87 bonds, 11 residues, 1 model selected
> color (#!1 & sel) magenta
> select #1/A:60
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:60-76
137 atoms, 138 bonds, 17 residues, 1 model selected
> color (#!1 & sel) lime
> select #1/B:60
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/B:60-76
124 atoms, 124 bonds, 17 residues, 1 model selected
> color (#!1 & sel) lime
> select clear
> select add #1
3005 atoms, 2704 bonds, 29 pseudobonds, 676 residues, 2 models selected
> select add #2
39065 atoms, 35152 bonds, 377 pseudobonds, 8788 residues, 29 models selected
> hide sel atoms
> select clear
> select add #1
3005 atoms, 2704 bonds, 29 pseudobonds, 676 residues, 2 models selected
> color (#!1 & sel) dark gray
> select #1/A:30
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:30-40
85 atoms, 87 bonds, 11 residues, 1 model selected
> color (#!1 & sel) magenta
> select #1/A:60-61
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A:60-76
137 atoms, 138 bonds, 17 residues, 1 model selected
> color (#!1 & sel) lime
> select #1/B:30
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:30-40
94 atoms, 96 bonds, 11 residues, 1 model selected
> color (#!1 & sel) magenta
> select #1/B:60
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/B:60-76
124 atoms, 124 bonds, 17 residues, 1 model selected
> color (#!1 & sel) lime
> select #1/B:30-40,60-76
218 atoms, 220 bonds, 28 residues, 1 model selected
> select sel @ select add #1
3132 atoms, 2786 bonds, 34 pseudobonds, 724 residues, 9 models selected
> select subtract #1
127 atoms, 82 bonds, 5 pseudobonds, 48 residues, 8 models selected
> show sel atoms
> hide sel cartoons
> show sel atoms
> hide sel cartoons
> select #1/A:30
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:30-40
85 atoms, 87 bonds, 11 residues, 1 model selected
> select clear
> select #1/A:30
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:30-40
85 atoms, 87 bonds, 11 residues, 1 model selected
> select #1/A:30-40,60-76
222 atoms, 225 bonds, 28 residues, 1 model selected
> select sel @ select add #1
3128 atoms, 2780 bonds, 31 pseudobonds, 727 residues, 10 models selected
> select subtract #1
123 atoms, 76 bonds, 2 pseudobonds, 51 residues, 9 models selected
> show sel atoms
> hide sel cartoons
> select add #2
36060 atoms, 32448 bonds, 348 pseudobonds, 8112 residues, 25 models selected
> hide sel cartoons
> select clear
> select ::name="HOH"
4368 atoms, 4368 residues, 13 models selected
> hide sel atoms
> select #1/A:30
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:30-40
85 atoms, 87 bonds, 11 residues, 1 model selected
> select #1/A:30-40,60-76
222 atoms, 225 bonds, 28 residues, 1 model selected
> select sel : select sel : select add #1
3845 atoms, 3452 bonds, 34 pseudobonds, 832 residues, 10 models selected
> select subtract #1
840 atoms, 748 bonds, 5 pseudobonds, 156 residues, 9 models selected
> show sel atoms
> hide sel cartoons
> select clear
> select add #1
3005 atoms, 2704 bonds, 29 pseudobonds, 676 residues, 2 models selected
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> select #1/A:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right distance
> distance #2.1/A:41@NH2 #1/A:31@OE1
Distance between 7jii.pdb -1 0 0 #2.1/A ARG 41 NH2 and 7jii.pdb #1/A GLU 31
OE1: 9.952Å
> ~distance #2.1/A:41@NH2 #1/A:31@OE1
> select clear
> select #1/A:30-31
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:30-40
85 atoms, 87 bonds, 11 residues, 1 model selected
> select #1/A:30-40,60-76
222 atoms, 225 bonds, 28 residues, 1 model selected
> select sel : show sel atoms
> hide sel cartoons
> show sel atoms
> hide sel cartoons
> hide sel atoms
> select add #1
3228 atoms, 2890 bonds, 32 pseudobonds, 727 residues, 10 models selected
> select subtract #1
223 atoms, 186 bonds, 3 pseudobonds, 51 residues, 9 models selected
> show sel atoms
> undo
Mismatch between Cocoa '\x0' and Carbon 'z' for virtual key 6 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'Z' for virtual key 6 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'z' for virtual key 6 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'Z' for virtual key 6 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u03a9' for virtual key 6 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b8' for virtual key 6 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u03a9' for virtual key 6 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b8' for virtual key 6 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select clear
> select ::name="HOH"
4368 atoms, 4368 residues, 13 models selected
> select clear
> select ::name="HOH"
4368 atoms, 4368 residues, 13 models selected
> delete atoms sel
> delete bonds sel
> select clear
> select #1/A:30
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:30-40
85 atoms, 87 bonds, 11 residues, 1 model selected
> select #1/A:30-40,60-76
222 atoms, 225 bonds, 28 residues, 1 model selected
> select clear
> select add #2
32028 atoms, 32448 bonds, 120 pseudobonds, 4080 residues, 25 models selected
> hide sel atoms
> select clear
> select #1/A:30-31
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:30-40
85 atoms, 87 bonds, 11 residues, 1 model selected
> select #1/A:30-40,60-76
222 atoms, 225 bonds, 28 residues, 1 model selected
> select sel : select add #1
2865 atoms, 2890 bonds, 13 pseudobonds, 364 residues, 10 models selected
> select subtract #1
196 atoms, 186 bonds, 3 pseudobonds, 24 residues, 9 models selected
> show sel atoms
> select clear
> select ::name="CA"::name="GDP"::name="MG"
806 atoms, 780 bonds, 26 pseudobonds, 104 residues, 26 models selected
> delete atoms (#!1#!2.1-12 & sel)
> delete bonds (#!1#!2.1-12 & sel)
> select clear
> select add #2
31284 atoms, 31728 bonds, 3984 residues, 13 models selected
> color sel blue
> select clear
> select #1/B:30
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:30-40
94 atoms, 96 bonds, 11 residues, 1 model selected
> select #1/B:30-40,60-76
218 atoms, 220 bonds, 28 residues, 1 model selected
> select sel : select add #1
2845 atoms, 2874 bonds, 359 residues, 7 models selected
> select subtract #1
238 atoms, 230 bonds, 27 residues, 7 models selected
> show sel atoms
> select clear
> select add #1
2607 atoms, 2644 bonds, 332 residues, 1 model selected
> show sel surfaces
> select clear
> set bgColor white
> save "/Users/apple/Documents/NYU_Langone/Koide_Lab/For RAS
> grant/crystal_contacts2/7jii_P1.cxs"
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8.dev202403290055 (2024-03-29)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,6
Model Number: MNWA3LL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 8422.121.1
OS Loader Version: 8422.121.1
Software:
System Software Overview:
System Version: macOS 13.4 (22F66)
Kernel Version: Darwin 22.5.0
Time since boot: 9 days, 19 hours, 28 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 38
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2413:
Resolution: 1200 x 1920
UI Looks like: 1200 x 1920 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: 90
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
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: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202403290055
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
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: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
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: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
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: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
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: 1.0
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: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
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: 1.37.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
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: 2.0.0
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: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in python_instances_of_class |
comment:2 by , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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