![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16826 closed defect (duplicate)
Crash moving window between screens
| 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-13.6-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 0x00000001e2292080 (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.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, 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.surface._surface, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 60)
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"procRole" : "Foreground",
"version" : 2,
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"modelCode" : "Mac14,9",
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"incident" : "CB2F2777-DA2A-44E0-BE1B-3E1426F76AB2",
"pid" : 50139,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-07 13:22:41.8923 +0100",
"procStartAbsTime" : 1206051324927,
"procExitAbsTime" : 3424037725245,
"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"},
"storeInfo" : {"deviceIdentifierForVendor":"0DE250B6-9F09-5709-9E32-E77FC34A864B","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "00104045-B26D-5210-4E6C-EDBFC16BA41A",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 31867,
"sleepWakeUUID" : "97317AF5-0BCD-454E-BD1B-4BE7F19CC54B",
"sip" : "enabled",
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"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":50139},
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 105554055790231\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600038000000-600040000000 [128.0M] rw-\/rwx SM=PRV ",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqtga.dylib",
"name" : "libqtga.dylib"
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{
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"uuid" : "8659aa4e-a5dd-30ef-9dcb-66fb8dff410e",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqmacjp2.dylib",
"name" : "libqmacjp2.dylib"
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{
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"uuid" : "106e99a0-0b8d-34fb-ad61-91eca3d8285c",
"path" : "\/usr\/lib\/libobjc-trampolines.dylib",
"name" : "libobjc-trampolines.dylib"
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{
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"uuid" : "94921430-81c9-39ce-b5ef-78d1a90b407d",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/iconengines\/libqsvgicon.dylib",
"name" : "libqsvgicon.dylib"
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{
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"size" : 81920,
"uuid" : "703104dc-b212-3b8d-9c78-4f57b3c9cb18",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/numpy_formathandler.cpython-311-darwin.so",
"name" : "numpy_formathandler.cpython-311-darwin.so"
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{
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"arch" : "arm64",
"base" : 5718507520,
"size" : 49152,
"uuid" : "12c53516-421d-3f7a-a81e-95bcfdb8a3ff",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/nones_formathandler.cpython-311-darwin.so",
"name" : "nones_formathandler.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
"base" : 11417337856,
"size" : 147456,
"uuid" : "1e310bc7-5f96-396b-816d-5b40a3dde12c",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
"name" : "_pdbio.cpython-311-darwin.so"
},
{
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"base" : 11004444672,
"size" : 81920,
"uuid" : "3133c77c-8bf7-32a3-b5db-cbfe2e50ce9d",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
"name" : "_ribbons.cpython-311-darwin.so"
},
{
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"base" : 11004280832,
"size" : 16384,
"uuid" : "de871a78-14f2-3e72-9bde-e4f2c7493f1b",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
"name" : "_graphics.cpython-311-darwin.so"
},
{
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"uuid" : "0c6e9a11-e483-3d7d-a88f-8ad0507af167",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
"name" : "mmcif.cpython-311-darwin.so"
},
{
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"uuid" : "1ab8e5e2-c699-3efb-8f77-d375e3793c8f",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
"name" : "_mmcif.cpython-311-darwin.so"
},
{
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"uuid" : "d7bd530c-3353-37a6-b81f-ee3179d65811",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/_version.cpython-311-darwin.so",
"name" : "_version.cpython-311-darwin.so"
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{
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/frame\/_frame.cpython-311-darwin.so",
"name" : "_frame.cpython-311-darwin.so"
},
{
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"uuid" : "c1a3c2d3-b21b-3231-839d-fcbc83ca2028",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_serialize.cpython-311-darwin.so",
"name" : "_serialize.cpython-311-darwin.so"
},
{
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"base" : 11385241600,
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"uuid" : "650aead6-ce16-39bb-9ba1-4bf9986b96d6",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so",
"name" : "_cmsgpack.cpython-311-darwin.so"
},
{
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"base" : 11388387328,
"size" : 737280,
"uuid" : "cc06500d-d418-3365-b197-36b1304a819e",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGL.abi3.so",
"name" : "QtOpenGL.abi3.so"
},
{
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"uuid" : "b32a8c32-a5e0-3a8b-9a0d-00a26b160215",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so",
"name" : "QtOpenGLWidgets.abi3.so"
},
{
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"base" : 11385618432,
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"uuid" : "cd4f396b-89fe-36fd-a488-6f5b3d4b0282",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGLWidgets.framework\/Versions\/A\/QtOpenGLWidgets",
"name" : "QtOpenGLWidgets"
},
{
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"base" : 11564810240,
"size" : 3817472,
"uuid" : "579ef19c-6e85-36be-a566-c980f789fbc0",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
"name" : "etree.cpython-311-darwin.so"
},
{
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"base" : 11393974272,
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"uuid" : "c8b24269-c8a2-3244-b044-b85c3449800d",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
"name" : "_elementpath.cpython-311-darwin.so"
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{
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"uuid" : "8abbdcef-1901-3d4b-9e6b-a38214b79214",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
"name" : "_imagingmath.cpython-311-darwin.so"
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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/rebaur/Team Nicolas Thoma Dropbox/Regina
> Baur/KBTBD4_PP2A_Structure/250206_K4_PP2A_rightPP2AseqAfIsol-LOOPScOOT.pdb"
Chain information for 250206_K4_PP2A_rightPP2AseqAfIsol-LOOPScOOT.pdb #1
---
Chain | Description
A B | No description available
C D | No description available
> open "/Users/rebaur/Team Nicolas Thoma Dropbox/Regina
> Baur/KBTBD4_PP2A_Structure/250205_KD4PA_C2symMap_Isolde.cxs"
Opened cryosparc_P2_J497_003_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.08, shown at level 0.128, step 1, values float32
Opened cryosparc_P2_J493_003_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.08, shown at level 0.194, step 1, values float32
opened ChimeraX session
> hide #!3 models
> hide #1 models
> show #1 models
> open "/Users/rebaur/Team Nicolas Thoma Dropbox/Regina
> Baur/KBTBD4_PP2A_Structure/250206_K4_PP2A_rightPP2AseqAfIsol-LOOPScOOT.pdb"
Chain information for 250206_K4_PP2A_rightPP2AseqAfIsol-LOOPScOOT.pdb #4
---
Chain | Description
A B | No description available
C D | No description available
> hide #4 models
> hide #1 models
> show #4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #1 models
> hide #!3 models
> hide #1 models
> show #!3 models
> hide #!3 models
> select #1/A#4/A
11993 atoms, 12167 bonds, 1018 residues, 2 models selected
> color (#4 & sel) light sea green
> select #1/B#4/B
11993 atoms, 12167 bonds, 1018 residues, 2 models selected
> color (#4 & sel) cornflower blue
> select #A
Expected an objects specifier or a keyword
> select #A
Expected an objects specifier or a keyword
> select #A
Expected an objects specifier or a keyword
> select #b
Expected an objects specifier or a keyword
> open select /A
'select' has no suffix
> select /A
11993 atoms, 12167 bonds, 1018 residues, 2 models selected
> ui tool show "Color Actions"
> color sel medium blue
> color sel deep sky blue
> color sel cornflower blue
> color sel dodger blue
> select #1/C#4/C
13666 atoms, 13806 bonds, 1158 residues, 2 models selected
> color (#4 & sel) #f67cffff
> color (#4 & sel) #cb6bffff
> color (#4 & sel) #ea9fffff
> color (#4 & sel) #eb9effff
> select #1/D#4/D
13666 atoms, 13806 bonds, 1158 residues, 2 models selected
> ui tool show "Color Actions"
> color sel plum
> color sel thistle
> select #1/C#4/C
13666 atoms, 13806 bonds, 1158 residues, 2 models selected
> color sel light pink
> color sel plum
> show #!3 models
> hide #!3 models
> show #!3 models
> color zone #3 near #4 distance 5
> select /a
11993 atoms, 12167 bonds, 1018 residues, 2 models selected
> select /A
11993 atoms, 12167 bonds, 1018 residues, 2 models selected
> ui tool show "Color Actions"
> color sel sky blue
> color sel light steel blue
> select /B
11993 atoms, 12167 bonds, 1018 residues, 2 models selected
> ui tool show "Color Actions"
> color sel powder blue
> color zone #3 near #4 distance 5
> ~select
Nothing selected
> select /A:408
31 atoms, 31 bonds, 2 residues, 2 models selected
> transparency #3 60\
Missing or invalid "percent" argument: Expected a number
> transparency #3 60
> show sel & #4 atoms
> select up
129 atoms, 131 bonds, 10 residues, 2 models selected
> select up
11993 atoms, 12167 bonds, 1018 residues, 2 models selected
> select /A:409
31 atoms, 31 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> ui tool show "Side View"
> select /B:408-409
62 atoms, 64 bonds, 4 residues, 2 models selected
> show sel & #4 atoms
> 357408-409
Unknown command: 357408-409
> select /B:357
26 atoms, 24 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /A:357
26 atoms, 24 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /C:456
22 atoms, 20 bonds, 2 residues, 2 models selected
> select /C:468
30 atoms, 29 bonds, 2 residues, 2 models selected
> select /D:468
30 atoms, 29 bonds, 2 residues, 2 models selected
> select /D:469
15 atoms, 13 bonds, 2 residues, 2 models selected
> select /D:459
19 atoms, 17 bonds, 2 residues, 2 models selected
> select /D:453
21 atoms, 19 bonds, 2 residues, 2 models selected
> select /D:456
22 atoms, 20 bonds, 2 residues, 2 models selected
> select /D:459
19 atoms, 17 bonds, 2 residues, 2 models selected
> select /D:460
24 atoms, 22 bonds, 2 residues, 2 models selected
> select /D:462
34 atoms, 35 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> hide sel & #4 atoms
> select /D:458
33 atoms, 33 bonds, 2 residues, 2 models selected
> select /D:459
19 atoms, 17 bonds, 2 residues, 2 models selected
> select /D:461
18 atoms, 16 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /D:460
24 atoms, 22 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> hide sel & #4 atoms
> select /D:462
34 atoms, 35 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> hide sel & #4 atoms
> select /D:464
28 atoms, 27 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> color (#4 & sel) byhetero
> select /C:464
28 atoms, 27 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> color (#4 & sel) byhetero
> select /A
11993 atoms, 12167 bonds, 1018 residues, 2 models selected
> ui tool show "Color Actions"
> color sel pale violet red
> select /B
11993 atoms, 12167 bonds, 1018 residues, 2 models selected
> ui tool show "Color Actions"
> color sel orchid
> color zone #3 near #4 distance 5
> select /C
13666 atoms, 13806 bonds, 1158 residues, 2 models selected
> ui tool show "Color Actions"
> color sel sky blue
> select /D
13666 atoms, 13806 bonds, 1158 residues, 2 models selected
> color sel cornflower blue
> select /D
13666 atoms, 13806 bonds, 1158 residues, 2 models selected
> color zone #3 near #4 distance 5
> transparency #3 70
> ~select
Nothing selected
> color #3-4 byhetero
> se,ec
Unknown command: se,ec
> se,ec
Unknown command: se,ec
> se,ec
Unknown command: se,ec
> select /B
11993 atoms, 12167 bonds, 1018 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light coral
> color zone #3 near #4 distance 5
> select /A
11993 atoms, 12167 bonds, 1018 residues, 2 models selected
> ui tool show "Color Actions"
> color sel pale violet red
> select /C
13666 atoms, 13806 bonds, 1158 residues, 2 models selected
> color sel sky blue
> select /D
13666 atoms, 13806 bonds, 1158 residues, 2 models selected
> color sel cornflower blue
> select /D
13666 atoms, 13806 bonds, 1158 residues, 2 models selected
> color zone #3 near #4 distance 5
> transparency #3 70
> color (#4 & sel) byhetero
> ~select
Nothing selected
> select /D:417
26 atoms, 24 bonds, 2 residues, 2 models selected
> select /D:423
24 atoms, 22 bonds, 2 residues, 2 models selected
> select /D:424
19 atoms, 17 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /D:425
29 atoms, 29 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /A308/313:425
Nothing selected
> select /A308-313
Nothing selected
> select /A308-313
Nothing selected
> select /A:308-313
146 atoms, 146 bonds, 12 residues, 2 models selected
> select /B:308-313
146 atoms, 146 bonds, 12 residues, 2 models selected
> show sel & #4 atoms
> color (#4 & sel) byhetero
> hide #!3 models
> select /D:543
20 atoms, 18 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> show #!3 models
> select all
51318 atoms, 51946 bonds, 4352 residues, 8 models selected
> color (#4 & sel) byhetero
> ~select
Nothing selected
> select /D:461
18 atoms, 16 bonds, 2 residues, 2 models selected
> hide sel & #4 atoms
> select /C:461
18 atoms, 16 bonds, 2 residues, 2 models selected
> select /C:416
27 atoms, 25 bonds, 2 residues, 2 models selected
> select /C:424
19 atoms, 17 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /C:425
29 atoms, 29 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /C:426
23 atoms, 21 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /A:408
31 atoms, 31 bonds, 2 residues, 2 models selected
> select /A:405
20 atoms, 18 bonds, 2 residues, 2 models selected
> select /A:406
27 atoms, 25 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> hide sel & #4 atoms
> select /A:407
20 atoms, 18 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> hide sel & #4 cartoons
> show sel & #4 cartoons
> hide sel & #4 atoms
> select /C:426
23 atoms, 21 bonds, 2 residues, 2 models selected
> hide sel & #4 atoms
> select /A:326
38 atoms, 40 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /A:324
38 atoms, 40 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> hide sel & #4 atoms
> select /A:325
24 atoms, 22 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> hide #!3 models
> select /C:266
23 atoms, 21 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /D:266
23 atoms, 21 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> hide #4 models
> show #4 models
> show #!3 models
> select /D:265
29 atoms, 29 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /D:264
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> hide sel & #4 atoms
> select /D:183
30 atoms, 28 bonds, 2 residues, 2 models selected
> select /D:190
25 atoms, 23 bonds, 2 residues, 2 models selected
> select /D:187
18 atoms, 17 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /D:191
25 atoms, 24 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /B:323
20 atoms, 18 bonds, 2 residues, 2 models selected
> select /A:323
20 atoms, 18 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /A:324
38 atoms, 40 bonds, 2 residues, 2 models selected
> select /A:321
21 atoms, 19 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> hide sel & #4 atoms
> select /A:320
15 atoms, 13 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /A:319
22 atoms, 20 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> hide sel & #4 atoms
> select /A:320
15 atoms, 13 bonds, 2 residues, 2 models selected
> hide sel & #4 atoms
> select /A:265
35 atoms, 33 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /A:266
21 atoms, 19 bonds, 2 residues, 2 models selected
> select /A:24
Nothing selected
> select /A:264
17 atoms, 15 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /D:61
18 atoms, 17 bonds, 2 residues, 2 models selected
> select /D:68
26 atoms, 25 bonds, 2 residues, 2 models selected
> select /D:69
20 atoms, 18 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /D:70
23 atoms, 21 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> select /D:71
27 atoms, 25 bonds, 2 residues, 2 models selected
> show sel & #4 atoms
> hide #4 models
> volume #2 level 0.2761
> volume #2 level 0.2852
> show #4 models
> hide #!2 models
> save /Users/rebaur/Documents/POSTDOC/PROJECTS/KBTBD4/CRYO-
> EM/250124_KBTBD4-PP2A-A/250207_PP2A-coot.cxs
> color sel gray
> lighting full
> lighting soft
> view sel
> view
> ~select
Nothing selected
> save /Users/rebaur/Documents/POSTDOC/PROJECTS/KBTBD4/CRYO-
> EM/250124_KBTBD4-PP2A-A/250207_PP2A-coot.cxs
> open
> /Users/rebaur/Downloads/fold_2025_02_10_17_06/fold_2025_02_10_17_06_model_0.cif
Chain information for fold_2025_02_10_17_06_model_0.cif #5
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
===== 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
> open
> /Users/rebaur/Downloads/fold_2025_02_10_17_06/fold_2025_02_10_17_06_model_0.cif
Chain information for fold_2025_02_10_17_06_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 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: Mac14,9
Model Number: MPHE3SM/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8422.141.2
OS Loader Version: 8422.141.2
Software:
System Software Overview:
System Version: macOS 13.6 (22G120)
Kernel Version: Darwin 22.6.0
Time since boot: 5 days, 7 hours, 17 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL SE2723DS:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 75.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
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-Clipper: 0.24.0
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-ISOLDE: 1.9
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
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
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
more-itertools: 10.3.0
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
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
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
platformdirs: 4.2.2
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
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
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: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 9 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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