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Opened 4 months ago
Closed 4 months ago
#18105 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.7.2-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 0x00000001f4768f80 (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.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 61)
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"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac15,12",
"coalitionID" : 142329,
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"build" : "23H311",
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"captureTime" : "2025-06-30 18:17:29.7928 +0200",
"codeSigningMonitor" : 1,
"incident" : "1ACB5CEC-3277-4EC4-90B5-38BFC729D9BC",
"pid" : 97587,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-06-30 10:08:41.5589 +0200",
"procStartAbsTime" : 23021957430702,
"procExitAbsTime" : 23725825914064,
"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":"69AEABDF-0D7D-515C-A41F-DCC45B0C895F","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "3E8A3289-E23E-F62C-606A-0ADCE74B70CA",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 31786,
"sleepWakeUUID" : "B687A165-7B97-4169-B9CA-08A82F2CDEA5",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4328947712\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102068000-10206c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":97587},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4328947712\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102068000-10206c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/dario.guerrini/Library/CloudStorage/OneDrive-SharedLibraries-
> Htechnopole/Casañal - Documents/DGuerrini/AlphaFold/Ime4-Kar4
> Sup35-Sup45.cxs"
opened ChimeraX session
> open "/Users/dario.guerrini/Library/CloudStorage/OneDrive-SharedLibraries-
> Htechnopole/Casañal - Documents/DGuerrini/231115_misky.pdb"
231115_misky.pdb title:
\--- [more info...]
Chain information for 231115_misky.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> hide #1#!4 atoms
> show #1#!4 cartoons
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #1-3 to #4
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 231115_misky.pdb, chain A (#4) with
fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp_model_0.cif, chain A (#1),
sequence alignment score = 1850.1
RMSD between 230 pruned atom pairs is 1.057 angstroms; (across all 439 pairs:
27.748)
Matchmaker 231115_misky.pdb, chain A (#4) with
fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp_model_1.cif, chain A (#2),
sequence alignment score = 1851.8
RMSD between 230 pruned atom pairs is 1.009 angstroms; (across all 439 pairs:
20.993)
Matchmaker 231115_misky.pdb, chain A (#4) with
fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp_model_2.cif, chain A (#3),
sequence alignment score = 1853.7
RMSD between 235 pruned atom pairs is 0.993 angstroms; (across all 439 pairs:
31.793)
> color #1#!4 bychain
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> save "/Users/dario.guerrini/Library/CloudStorage/OneDrive-SharedLibraries-
> Htechnopole/Casañal - Documents/DGuerrini/AlphaFold/Ime4-Kar4
> Sup35-Sup45.cxs"
> ui tool show "AlphaFold Error Plot"
> alphafold pae #3 file
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp/fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp_full_data_2.json
> color #3/D:9-142 lime
> color #3/A:160-523 magenta
> hide #1 models
> show #3 models
> hide #3 models
> show #2 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #2 file
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp/fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp_full_data_1.json
> color #2/D:6-135 lime
> color #2/A:156-519 magenta
> hide #2 models
> show #1 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp/fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp_full_data_0.json
> color #1/D:10-139 lime
> color #1/A:164-519 magenta
> show #2 models
> hide #1 models
> show #1 models
> show #3 models
> hide #2 models
> hide #1 models
> hide #3 models
> show #3 models
> show #3 atoms
> hide #3 atoms
> interfaces #3 & ~solvent
5 buried areas: A B 4347, C D 2817, A D 1541, D B 773, C E 439
> color #3/D:1-140 lime
> color #3/B:39-330 magenta
> ui tool show "Side View"
> lighting soft
> graphics silhouettes true
> lighting simple
> lighting flat
> lighting soft
> lighting full
> lighting simple
> graphics silhouettes false
> set bgColor gray
> set bgColor black
> set bgColor white
> view
> save /Users/dario.guerrini/Desktop/image1.png supersample 3
> select clear
> paegreen #3
Unknown command: alphafold paegreen #3
> alphafold pae #3 paegreen
Expected a keyword
> color #3/D:5-137 lime
> color #3/A:164-519 magenta
> color #3/D:325 lime
> color #3/A:304 magenta
> color #3/D:5-143 lime
> color #3/A:156-519 magenta
> save /Users/dario.guerrini/Desktop/image1.png supersample 3
> ui tool show "AlphaFold Error Plot"
> alphafold pae #3 file
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp/fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp_full_data_2.json
> select #/A:160-519
Expected an objects specifier or a keyword
> select #/A 160-519
Expected an objects specifier or a keyword
> select #3/A:160-519
2911 atoms, 2979 bonds, 360 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orange
> select clear
> ui mousemode right select
> select #3/A:159
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel orange
> save /Users/dario.guerrini/Desktop/image1.png supersample 3
> save "/Users/dario.guerrini/Library/CloudStorage/OneDrive-SharedLibraries-
> Htechnopole/Casañal - Documents/DGuerrini/AlphaFold/Ime4-Kar4
> Sup35-Sup45.cxs"
> close session
> open "/Users/dario.guerrini/Library/CloudStorage/OneDrive-SharedLibraries-
> Htechnopole/Casañal -
> Documents/DGuerrini/AlphaFold/Cap_binding_complex_predictions.cxs"
opened ChimeraX session
> open
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_0.cif
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_1.cif
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_2.cif
Chain information for fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_0.cif #22
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
Chain information for fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_1.cif #23
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
Chain information for fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_2.cif #24
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
> close #22-24
> close #7-9
> close #1-3
> close #4-6
> close #16-18
> close #19-21
> open
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_0.cif
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_1.cif
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_2.cif
Chain information for fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
Chain information for fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_1.cif #2
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
Chain information for fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_2.cif #3
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
> open
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_model_0.cif
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_model_1.cif
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_model_2.cif
Chain information for
fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_model_0.cif #4
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
Chain information for
fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_model_1.cif #5
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
Chain information for
fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_model_2.cif #6
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
> open
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_model_0.cif
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_model_1.cif
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_model_2.cif
Chain information for
fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_model_0.cif #7
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
Chain information for
fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_model_1.cif #8
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
Chain information for
fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_model_2.cif #9
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
> open /Users/dario.guerrini/Library/CloudStorage/OneDrive-
> Htechnopole/231115_misky.pdb
231115_misky.pdb title:
\--- [more info...]
Chain information for 231115_misky.pdb #16
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> hide #1-9#!16 atoms
> show #1-9#!16 cartoons
Computing secondary structure
> color #1-9#!16 bychain
> ui tool show Matchmaker
> hide #!16 models
> show #!16 models
> ui tool show Matchmaker
> hide #!16 models
> hide #9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> hide #1 models
> ui tool show Matchmaker
> matchmaker #1-15 to #16
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 231115_misky.pdb, chain A (#16) with
fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_0.cif, chain A (#1), sequence
alignment score = 1862.1
RMSD between 245 pruned atom pairs is 0.998 angstroms; (across all 439 pairs:
19.437)
Matchmaker 231115_misky.pdb, chain A (#16) with
fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_1.cif, chain A (#2), sequence
alignment score = 1845.2
RMSD between 238 pruned atom pairs is 0.989 angstroms; (across all 439 pairs:
23.056)
Matchmaker 231115_misky.pdb, chain A (#16) with
fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_2.cif, chain A (#3), sequence
alignment score = 1868.1
RMSD between 236 pruned atom pairs is 1.023 angstroms; (across all 439 pairs:
17.912)
Matchmaker 231115_misky.pdb, chain A (#16) with
fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_model_0.cif, chain A
(#4), sequence alignment score = 1842.9
RMSD between 241 pruned atom pairs is 1.026 angstroms; (across all 439 pairs:
20.976)
Matchmaker 231115_misky.pdb, chain A (#16) with
fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_model_1.cif, chain A
(#5), sequence alignment score = 1852.4
RMSD between 248 pruned atom pairs is 0.938 angstroms; (across all 439 pairs:
22.851)
Matchmaker 231115_misky.pdb, chain A (#16) with
fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_model_2.cif, chain A
(#6), sequence alignment score = 1837.5
RMSD between 246 pruned atom pairs is 0.930 angstroms; (across all 439 pairs:
17.769)
Matchmaker 231115_misky.pdb, chain A (#16) with
fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_model_0.cif, chain A (#7),
sequence alignment score = 1820.7
RMSD between 242 pruned atom pairs is 0.944 angstroms; (across all 439 pairs:
21.197)
Matchmaker 231115_misky.pdb, chain A (#16) with
fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_model_1.cif, chain A (#8),
sequence alignment score = 1867.5
RMSD between 241 pruned atom pairs is 0.974 angstroms; (across all 439 pairs:
19.413)
Matchmaker 231115_misky.pdb, chain A (#16) with
fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_model_2.cif, chain A (#9),
sequence alignment score = 1860.3
RMSD between 244 pruned atom pairs is 1.007 angstroms; (across all 439 pairs:
24.652)
Matchmaker 231115_misky.pdb, chain C (#16) with
fold_eif4a_eif4g_eif4e_eif4b_model_0.cif, chain B (#10), sequence alignment
score = 225.1
RMSD between 17 pruned atom pairs is 0.666 angstroms; (across all 299 pairs:
28.385)
Matchmaker 231115_misky.pdb, chain C (#16) with
fold_eif4a_eif4g_eif4e_eif4b_model_1.cif, chain B (#11), sequence alignment
score = 241.2
RMSD between 18 pruned atom pairs is 0.768 angstroms; (across all 295 pairs:
32.752)
Matchmaker 231115_misky.pdb, chain C (#16) with
fold_eif4a_eif4g_eif4e_eif4b_model_2.cif, chain B (#12), sequence alignment
score = 226
RMSD between 18 pruned atom pairs is 0.789 angstroms; (across all 297 pairs:
31.804)
Matchmaker 231115_misky.pdb, chain D (#16) with
fold_eif4a_eif4g_eif4e_eif4b_rec8rna_model_0.cif, chain B (#13), sequence
alignment score = 222
RMSD between 10 pruned atom pairs is 1.526 angstroms; (across all 449 pairs:
35.979)
Matchmaker 231115_misky.pdb, chain C (#16) with
fold_eif4a_eif4g_eif4e_eif4b_rec8rna_model_1.cif, chain B (#14), sequence
alignment score = 220.2
RMSD between 18 pruned atom pairs is 0.802 angstroms; (across all 303 pairs:
31.143)
Matchmaker 231115_misky.pdb, chain C (#16) with
fold_eif4a_eif4g_eif4e_eif4b_rec8rna_model_2.cif, chain B (#15), sequence
alignment score = 220.2
RMSD between 14 pruned atom pairs is 0.824 angstroms; (across all 303 pairs:
39.656)
> show #!16 models
> select clear
> ui mousemode right translate
> show #1 models
> hide #1 models
> ui tool show "Side View"
> hide #!16 models
> show #1 models
> hide #1 models
> show #10 models
> hide #10 models
> show #!16 models
> select #16/A:160-519
2511 atoms, 2566 bonds, 4 pseudobonds, 308 residues, 2 models selected
> select clear
> show #1 models
> hide #1 models
> show #1 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_full_data_0.json
> color #1/F:365-371 lime
> color #1/B:35-47 magenta
> color #1/F:371-398 lime
> color #1/B:29-320 magenta
> hide #1 models
> show #4 models
> ui mousemode right pivot
> ui mousemode right translate
> ui tool show "AlphaFold Error Plot"
> alphafold pae #4 file
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_full_data_0.json
> color #4/D:568-917 lime
> color #4/B:35-329 magenta
> color #4/D:860-886 lime
> color #4/B:47-335/C:1-6 magenta
> color #4/G:11-24 lime
> color #4/B:40-335/C:1-2 magenta
> color #4/D:859-894 lime
> color #4/A:182-600/B:1-331 magenta
> color #4/D:566 lime
> color #4/B:140 magenta
> color #4/D:863-890 lime
> color #4/A:182-524 magenta
> select #4/G
605 atoms, 678 bonds, 28 residues, 1 model selected
> color sel cyan
> select #4/A:187-524
2731 atoms, 2797 bonds, 338 residues, 1 model selected
> color sel orange
> ui mousemode right select
> select #4/A:183
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #4/A:182
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #4/A:184
25 atoms, 22 bonds, 3 residues, 1 model selected
> select add #4/A:186
32 atoms, 28 bonds, 4 residues, 1 model selected
> select add #4/A:185
44 atoms, 40 bonds, 5 residues, 1 model selected
> color sel orange
> hide #4 models
> show #4 models
> hide #4 models
> show #1 models
> hide #1 models
> show #7 models
> hide #7 models
> show #4 models
> hide #4 models
> show #7 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #7 file
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_full_data_0.json
> color #7/E:36-213 lime
> color #7/A:178-511 magenta
Drag select of 9 residues
> undo
> ui mousemode right translate
> select clear
> color #7 bychain
> select #7/E:58
14 atoms, 15 bonds, 1 residue, 1 model selected
> 104
Unknown command: 104
> select #7/E:58-104
408 atoms, 424 bonds, 47 residues, 1 model selected
> ui mousemode right pivot
> ui mousemode right translate
> ui mousemode right select
> select #7/E:104
14 atoms, 15 bonds, 1 residue, 1 model selected
> select add #7/E:58
28 atoms, 30 bonds, 2 residues, 1 model selected
> show sel atoms
> hide sel surfaces
> hide sel atoms
> show sel atoms
> style sel stick
Changed 28 atom styles
> color sel red
> ui mousemode right translate
> select #7/G
606 atoms, 679 bonds, 28 residues, 1 model selected
> color sel cyan
> select #7/G:1
25 atoms, 27 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 25 atom styles
> lighting soft
> lighting flat
> select clear
> save /Users/dario.guerrini/Desktop/image1.png supersample 3
> hide #7 models
> show #1 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_full_data_0.json
> ui mousemode right pivot
> ui mousemode right translate
> save /Users/dario.guerrini/Desktop/image1.png supersample 3
> hide #1 models
> show #4 models
> save /Users/dario.guerrini/Desktop/image1.png supersample 3
> color #7/B:327 lime
> color #7/D:734 magenta
> color #4/C:68-164 lime
> color #4/A:177-524 magenta
> select #4/G
605 atoms, 678 bonds, 28 residues, 1 model selected
> color sel cyan
> select #4/A:182-523
2766 atoms, 2833 bonds, 342 residues, 1 model selected
> color sel orange
> select clear
> ui mousemode right select
> select #4/A:179
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/A:181
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:180
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #4/A:181
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #4/A:179
23 atoms, 20 bonds, 3 residues, 1 model selected
> select subtract #4/A:179
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #4/A:524
27 atoms, 24 bonds, 3 residues, 1 model selected
> color sel orange
> select #4/A:179
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #4/A:178
13 atoms, 11 bonds, 2 residues, 1 model selected
> color sel orange
Drag select of 6 residues
> select clear
> ui mousemode right translate
> select clear
> color #4 bychain
> select #4/G
605 atoms, 678 bonds, 28 residues, 1 model selected
> color sel cyan
> select clear
> select #4/G
605 atoms, 678 bonds, 28 residues, 1 model selected
> select #4/G
605 atoms, 678 bonds, 28 residues, 1 model selected
> select #4/G zr select sel : show sel
> hide ~sel
> select ~sel & ##selected
301817 atoms, 308352 bonds, 34 pseudobonds, 37680 residues, 16 models selected
> hide sel & #4 cartoons
> undo
> select ~sel & ##selected
12751 atoms, 12876 bonds, 1348 residues, 15 models selected
> select clear
> select #4/G
605 atoms, 678 bonds, 28 residues, 1 model selected
> select sel : select sel : select ~sel & ##selected
236993 atoms, 242530 bonds, 30 pseudobonds, 29735 residues, 17 models selected
> hide sel & #4 cartoons
> select #4/G:1
24 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 24 atom styles
> select clear
> select #4/E:58
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> color sel red
> select #4/E:104
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> color sel red
> save /Users/dario.guerrini/Desktop/image1.png supersample 3
> hide #4 models
> show #1 models
> show #7 models
> hide #1 models
> color #7 bychain
> select #7/G
606 atoms, 679 bonds, 28 residues, 1 model selected
> color sel cyan
> select sel : select ~sel & ##selected
284223 atoms, 290558 bonds, 34 pseudobonds, 35505 residues, 16 models selected
> hide sel & #7 cartoons
> undo
> select #7/G
606 atoms, 679 bonds, 28 residues, 1 model selected
> select sel : select sel : select ~sel & ##selected
199921 atoms, 204652 bonds, 27 pseudobonds, 25043 residues, 17 models selected
> hide sel & #7 cartoons
> select #7/G:1
25 atoms, 27 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 25 atom styles
> select #7/E:58
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> select #7/E:104
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel red
> show sel atoms
> style sel stick
Changed 14 atom styles
> save /Users/dario.guerrini/Desktop/image1.png supersample 3
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3
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 Air
Model Identifier: Mac15,12
Model Number: Z1B8001FCT/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.140.19.700.2
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7.2 (23H311)
Kernel Version: Darwin 23.6.0
Time since boot: 35 days, 21 hours, 26 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 4 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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