![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16683 closed defect (limitation)
QObject::killTimer: Timers cannot be stopped from another thread
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | chimera-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.10.dev202501230202 (2025-01-23 02:02:02 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x00001e28 (most recent call first):
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\site-packages\chimerax\core\__main__.py", line 1050 in init
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\site-packages\chimerax\core\__main__.py", line 1213 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: _win32sysloader, win32api, win32com.shell.shell, 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, psutil._psutil_windows, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, 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, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.atom_search.ast (total: 61)
===== Log before crash start =====
UCSF ChimeraX version: 1.10.dev202501230202 (2025-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open C:\\\Users\\\zhyau\\\OneDrive\\\Desktop\\\2.cxs
Log from Thu Jan 23 15:06:07 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:\Users\zhyau\OneDrive\Desktop\2.cxs format session
Log from Thu Jan 23 13:17:21 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:\\\Users\\\zhyau\\\OneDrive\\\Desktop\\\2.cxs
Log from Thu Jan 23 11:55:14 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:/Users/zhyau/OneDrive/Desktop/2.cxs
Log from Wed Jan 22 22:30:09 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:/Users/zhyau/OneDrive/Desktop/2.cxs
Log from Wed Jan 22 15:05:40 2025 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 C:\\\Users\\\zhyau\\\OneDrive\\\Desktop\\\I.cif
Chain information for I.cif #1
---
Chain | Description
A B C D | .
E F G H | .
> hide all
> select /A,E
9604 atoms, 9814 bonds, 1212 residues, 1 model selected
> SHOW
Unknown command: SHOW
> show
> hide all
> show /A,E
> select clear
> select #1/B: select #1/E: style sel stick
Changed 122 atom styles
> select #1/A: style sel stick
Changed 170 atom styles
> select up
Computing secondary structure
586 atoms, 593 bonds, 74 residues, 1 model selected
> select up
2919 atoms, 2975 bonds, 373 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select /A:737@O
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
111 atoms, 114 bonds, 12 residues, 1 model selected
> select up
6685 atoms, 6839 bonds, 839 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select #1/A: style sel stick
Changed 170 atom styles
> show sel atoms
> select #1/E: show sel atoms
> color sel red
> select #1/A: color sel cyan
> ui tool show "Add Hydrogens"
> addh
Summary of feedback from adding hydrogens to I.cif #1
---
notes | Termini for I.cif (#1) chain A determined from SEQRES records
Termini for I.cif (#1) chain B determined from SEQRES records
Termini for I.cif (#1) chain C determined from SEQRES records
Termini for I.cif (#1) chain D determined from SEQRES records
Termini for I.cif (#1) chain E determined from SEQRES records
3 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C MET
1, /D MET 1, /E MET 1, /F MET 1, /G MET 1, /H MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A LYS 839, /B LYS 839, /C LYS
839, /D LYS 839, /E LYS 373, /F LYS 373, /G LYS 373, /H LYS 373
Chain-final residues that are not actual C termini:
4217 hydrogen bonds
38136 hydrogens added
> color blue @N
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color red @O
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color atoms blue @N
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color ribbons green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> save C:/Users/zhyau/Desktop/2.cxs
——— End of log from Wed Jan 22 15:05:40 2025 ———
opened ChimeraX session
> color sel byelement
> select #1/E: color sel byelement
> hide H
> save C:/Users/zhyau/OneDrive/Desktop/2.cxs
> select clear
> select /A:170@NE2
1 atom, 1 residue, 1 model selected
> select clear
> select /A:170@NE2
1 atom, 1 residue, 1 model selected
> select /E:281@OH
1 atom, 1 residue, 1 model selected
> select /A:170@NE2
1 atom, 1 residue, 1 model selected
> select /E:281@OH
1 atom, 1 residue, 1 model selected
> select add /A:170@NE2
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /E:281@OH /A:170@NE2
Distance between /E TYR 281 OH and /A GLN 170 NE2: 6.194Å
> distance style decimalPlaces 4
[Repeated 2 time(s)]
> select /A:183@NZ
1 atom, 1 residue, 1 model selected
> select /A:183@NZ
1 atom, 1 residue, 1 model selected
> select /E:329@OD1
1 atom, 1 residue, 1 model selected
> select /E:329@OD1
1 atom, 1 residue, 1 model selected
> select /E:329@OD1
1 atom, 1 residue, 1 model selected
> select /A:183@NZ
1 atom, 1 residue, 1 model selected
> select add /E:329@OD1
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /A:183@NZ /E:329@OD1
Distance between /A LYS 183 NZ and /E ASP 329 OD1: 3.3356Å
> save C:/Users/zhyau/OneDrive/Desktop/2.cxs
> select /E:329@OD2
1 atom, 1 residue, 1 model selected
> select add /E:284@OH
2 atoms, 2 residues, 1 model selected
> select subtract /E:284@OH
1 atom, 1 residue, 1 model selected
> select /E:284@OH
1 atom, 1 residue, 1 model selected
> select add /E:329@OD2
2 atoms, 2 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> ui tool show Distances
> distance /E 281O &/ A:170N
Unknown command: measure distance /E 281O &/ A:170N
> distance :281@O @A:170@N
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 16 atoms and 0
measurable objects
> distance :281@O @A:170@N
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 16 atoms and 0
measurable objects
> select /E:154
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /E:294
16 atoms, 15 bonds, 1 residue, 1 model selected
> label :sel text "ID: %r, Type: %aa"
> undo
> select /E:291
24 atoms, 23 bonds, 1 residue, 1 model selected
> label :sel text "ID: %r, Type: %aa"
> label selected size 20 color yellow text "ID: %r, Type: %aa"
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label sel size 20 color yellow text "ID: %r, Type: %aa"
> save C:/Users/zhyau/OneDrive/Desktop/2.cxs
——— End of log from Wed Jan 22 22:30:09 2025 ———
opened ChimeraX session
> select /E:85
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
73 atoms, 74 bonds, 4 residues, 1 model selected
> select up
5787 atoms, 5843 bonds, 373 residues, 1 model selected
> select down
73 atoms, 74 bonds, 4 residues, 1 model selected
> select down
22 atoms, 21 bonds, 1 residue, 1 model selected
> select down
22 atoms, 21 bonds, 1 residue, 1 model selected
> select down
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B /C /D
Alignment identifier is 1
> select /A-D:1
76 atoms, 72 bonds, 4 residues, 1 model selected
> select /A-D:1-68
4020 atoms, 4088 bonds, 272 residues, 1 model selected
> select /A-D:1
76 atoms, 72 bonds, 4 residues, 1 model selected
> select /A-D:1-114
6720 atoms, 6808 bonds, 456 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain /E /F /G /H
Alignment identifier is 2
> select /E-H:1
76 atoms, 72 bonds, 4 residues, 1 model selected
> select /E-H:1-5
348 atoms, 344 bonds, 20 residues, 1 model selected
> select /E-H:1
76 atoms, 72 bonds, 4 residues, 1 model selected
> select /E-H:1-67
4060 atoms, 4108 bonds, 268 residues, 1 model selected
> select /E-H:1
76 atoms, 72 bonds, 4 residues, 1 model selected
> select /E-H:1-198
12384 atoms, 12532 bonds, 792 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /E-H:228
28 atoms, 24 bonds, 4 residues, 1 model selected
> select /E-H:228-261
1764 atoms, 1776 bonds, 136 residues, 1 model selected
> select
> /E-H:11-22,25-36,41-48,92-100,105-115,118-128,148-155,160-170,176-187,199-208,217-227
7388 atoms, 7420 bonds, 460 residues, 1 model selected
> select /E-H:217
68 atoms, 68 bonds, 4 residues, 1 model selected
> select /E-H:217-227
692 atoms, 696 bonds, 44 residues, 1 model selected
> select /E-H:199
68 atoms, 68 bonds, 4 residues, 1 model selected
> select /E-H:199-227
1832 atoms, 1848 bonds, 116 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /A:279
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> color sel byhetero
> ui tool show "Color Actions"
> color sel cadet blue
> color sel steel blue
> color sel slate gray
> color sel dark cyan
> color sel cornflower blue
> color sel medium aquamarine
[Repeated 1 time(s)]
> color sel steel blue
> color sel cadet blue
[Repeated 1 time(s)]
> color sel light slate gray
[Repeated 1 time(s)]
> color sel slate gray
[Repeated 2 time(s)]
> color sel light slate gray
> color sel medium aquamarine
> color sel teal
> color sel steel blue
[Repeated 1 time(s)]
> color sel cadet blue
> color sel light slate gray
> select clear
> select /A:277
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel light slate gray
> hide sel atoms
> select /A:227
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:320
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:321
17 atoms, 17 bonds, 1 residue, 1 model selected
> hide sel cartoons
> undo
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select /A:323
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> color sel light slate gray
> select /A:320
19 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
> select /A:321
17 atoms, 17 bonds, 1 residue, 1 model selected
> select /A:762
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:321
17 atoms, 17 bonds, 1 residue, 1 model selected
> select add /A:320
36 atoms, 35 bonds, 2 residues, 1 model selected
> color sel light slate gray
> select /A:227
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel light slate gray
> view
> save C:/Users/zhyau/OneDrive/Desktop/2.cxs
——— End of log from Thu Jan 23 11:55:14 2025 ———
opened ChimeraX session
> select /A:161
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
117 atoms, 116 bonds, 7 residues, 1 model selected
> select up
13351 atoms, 13505 bonds, 839 residues, 1 model selected
> show sel surface'
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sel surfaces
> select /A-D:1
76 atoms, 72 bonds, 4 residues, 1 model selected
> select /A-D:1-110
6416 atoms, 6500 bonds, 440 residues, 1 model selected
> select /A-D:114
48 atoms, 44 bonds, 4 residues, 1 model selected
> select /A-D:1-114
6720 atoms, 6808 bonds, 456 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> select /A:332@CG
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 1 residue, 2 models selected
> select up
131 atoms, 130 bonds, 8 residues, 2 models selected
> select up
13351 atoms, 13505 bonds, 839 residues, 2 models selected
> transparency (#!1 & sel) 80
> select clear
> select /A-D:98
44 atoms, 40 bonds, 4 residues, 1 model selected
> select /A-D:97-98
100 atoms, 96 bonds, 8 residues, 1 model selected
> select /A-D:115
96 atoms, 92 bonds, 4 residues, 1 model selected
> select /A-D:115-353
14924 atoms, 15032 bonds, 956 residues, 1 model selected
> select /A-D:115
96 atoms, 92 bonds, 4 residues, 1 model selected
> select /A-D:115-383
16936 atoms, 17084 bonds, 1076 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /E /F /G /H
Alignment identifier is 2
> select /E-H:1
76 atoms, 72 bonds, 4 residues, 1 model selected
> select /E-H:1-125
7840 atoms, 7936 bonds, 500 residues, 1 model selected
> select /E-H:154
40 atoms, 36 bonds, 4 residues, 1 model selected
> select /E-H:154-345
11696 atoms, 11792 bonds, 768 residues, 1 model selected
> select /E-H:154
40 atoms, 36 bonds, 4 residues, 1 model selected
> select /E-H:154-373
13512 atoms, 13612 bonds, 880 residues, 1 model selected
> select /A-D:675-676
152 atoms, 148 bonds, 8 residues, 1 model selected
> select /A-D:675-772
6380 atoms, 6436 bonds, 392 residues, 1 model selected
> select /A-D:647
48 atoms, 44 bonds, 4 residues, 1 model selected
> select /A-D:647-650
264 atoms, 264 bonds, 16 residues, 1 model selected
> select /A-D:839
92 atoms, 88 bonds, 4 residues, 1 model selected
> select /A-D:749-839
5700 atoms, 5764 bonds, 364 residues, 1 model selected
> select /A-D:252
56 atoms, 56 bonds, 4 residues, 1 model selected
> select /A-D:252-346
5816 atoms, 5856 bonds, 380 residues, 1 model selected
> select /A-D:367
44 atoms, 40 bonds, 4 residues, 1 model selected
> select /A-D:367-461
6308 atoms, 6404 bonds, 380 residues, 1 model selected
> select /A-D:158
44 atoms, 40 bonds, 4 residues, 1 model selected
> select /A-D:158-283
7848 atoms, 7912 bonds, 504 residues, 1 model selected
> select /A-D:1
76 atoms, 72 bonds, 4 residues, 1 model selected
> select /A-D:1-175
10588 atoms, 10696 bonds, 700 residues, 1 model selected
> save C:/Users/zhyau/OneDrive/Desktop/2.cxs
> ui tool show "Color Actions"
> ui tool show "Basic Actions"
> ui tool show "Render/Select by Attribute"
> cartoon style (#!1 & sel) xsection rectangle modeHelix default
> undo
> cartoon style (#!1 & sel) xsection oval modeHelix default
> undo
> cartoon style (#!1 & sel & coil) xsection oval
> cartoon style (#!1 & sel) xsection barbell modeHelix default
> undo
> cartoon style (#!1 & sel) modeHelix tube sides 20
> undo
> cartoon style (#!1 & sel) modeHelix tube sides 20
> undo
> show sel tube helix
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sel tube helices
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select up
11164 atoms, 11272 bonds, 732 residues, 2 models selected
> select up
53404 atoms, 54020 bonds, 3356 residues, 2 models selected
> select down
11164 atoms, 11272 bonds, 732 residues, 2 models selected
> select down
10588 atoms, 10696 bonds, 700 residues, 2 models selected
Drag select of I.cif_A SES surface, 49531 of 1181730 triangles, 63 residues
> cartoon style (#!1 & sel) modeHelix tube sides 20
> undo
> select #1/E:50-100
826 atoms, 843 bonds, 51 residues, 1 model selected
> select #1/E:152-200
758 atoms, 766 bonds, 49 residues, 1 model selected
> select #1/E:500-700
Nothing selected
> select #1/A:500-700
3299 atoms, 3338 bonds, 201 residues, 1 model selected
> cartoon style (#!1 & sel) modeHelix tube sides 20
> undo
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #1.2 models
> show #1.2 models
> hide #1.1 models
> show #1.1 models
> save C:/Users/zhyau/OneDrive/Desktop/2.cxs
——— End of log from Thu Jan 23 13:17:21 2025 ———
opened ChimeraX session
> select helix
34374 atoms, 34532 bonds, 2066 residues, 1 model selected
> select clear
> select backbone
29212 atoms, 29204 bonds, 4848 residues, 1 model selected
> select clear
> select ~sel & ##selected
Nothing selected
> select /E:295
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
162 atoms, 162 bonds, 10 residues, 1 model selected
> select up
5787 atoms, 5843 bonds, 373 residues, 1 model selected
> color sel lime
> color sel byelement
> select /A:269@O
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 2 models selected
> select up
161 atoms, 161 bonds, 9 residues, 2 models selected
> select up
13351 atoms, 13505 bonds, 839 residues, 2 models selected
> color (#!1 & sel) orange
> transparency (#!1 & sel) 80
> set bgColor white
> hide #!2 models
> hide #2.1 models
> hide #!1 models
> show #!1 models
> save C:/Users/zhyau/OneDrive/Desktop/2.cxs
——— End of log from Thu Jan 23 15:06:07 2025 ———
> view name session-start
opened ChimeraX session
> select #1/E: color (#!1 & sel) red
> ui tool show Clashes
> clashes ignoreHiddenModels true
835 clashes
> ui tool show Contacts
> contacts ignoreHiddenModels true makePseudobonds false
48498 contacts
> contacts ignoreHiddenModels true color #000000
48498 contacts
> contacts ignoreHiddenModels true color #000000
48498 contacts
> contacts ignoreHiddenModels true color #000000
48498 contacts
> contacts ignoreHiddenModels true color #000000
48498 contacts
> contacts ignoreHiddenModels true color #000000
48498 contacts
> select /E:284
21 atoms, 21 bonds, 1 residue, 1 model selected
> measure center sel mark true radius 0.3 color cyan
Center of mass of 21 atoms = (16.19, 46.17, -14.81)
QObject::killTimer: Timers cannot be stopped from another thread
QObject::~QObject: Timers cannot be stopped from another thread
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.dev202501230202 (2025-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open C:\\\Users\\\zhyau\\\OneDrive\\\Desktop\\\2.cxs
Log from Thu Jan 23 15:06:07 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:\Users\zhyau\OneDrive\Desktop\2.cxs format session
Log from Thu Jan 23 13:17:21 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:\\\Users\\\zhyau\\\OneDrive\\\Desktop\\\2.cxs
Log from Thu Jan 23 11:55:14 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:/Users/zhyau/OneDrive/Desktop/2.cxs
Log from Wed Jan 22 22:30:09 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:/Users/zhyau/OneDrive/Desktop/2.cxs
Log from Wed Jan 22 15:05:40 2025 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 C:\\\Users\\\zhyau\\\OneDrive\\\Desktop\\\I.cif
Chain information for I.cif #1
---
Chain | Description
A B C D | .
E F G H | .
> hide all
> select /A,E
9604 atoms, 9814 bonds, 1212 residues, 1 model selected
> SHOW
Unknown command: SHOW
> show
> hide all
> show /A,E
> select clear
> select #1/B:<3.5 & #1/A
Nothing selected
> select #1/E:<3.5 & #1/A
122 atoms, 112 bonds, 15 residues, 1 model selected
> style sel stick
Changed 122 atom styles
> select #1/A:<3.5 & #1/E
170 atoms, 164 bonds, 18 residues, 1 model selected
> style sel stick
Changed 170 atom styles
> select up
Computing secondary structure
586 atoms, 593 bonds, 74 residues, 1 model selected
> select up
2919 atoms, 2975 bonds, 373 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select /A:737@O
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
111 atoms, 114 bonds, 12 residues, 1 model selected
> select up
6685 atoms, 6839 bonds, 839 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select #1/A:<3.5 & #1/E
170 atoms, 164 bonds, 18 residues, 1 model selected
> style sel stick
Changed 170 atom styles
> show sel atoms
> select #1/E:<3.5 & #1/A
122 atoms, 112 bonds, 15 residues, 1 model selected
> show sel atoms
> color sel red
> select #1/A:<3.5 & #1/E
170 atoms, 164 bonds, 18 residues, 1 model selected
> color sel cyan
> ui tool show "Add Hydrogens"
> addh
Summary of feedback from adding hydrogens to I.cif #1
---
notes | Termini for I.cif (#1) chain A determined from SEQRES records
Termini for I.cif (#1) chain B determined from SEQRES records
Termini for I.cif (#1) chain C determined from SEQRES records
Termini for I.cif (#1) chain D determined from SEQRES records
Termini for I.cif (#1) chain E determined from SEQRES records
3 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C MET
1, /D MET 1, /E MET 1, /F MET 1, /G MET 1, /H MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A LYS 839, /B LYS 839, /C LYS
839, /D LYS 839, /E LYS 373, /F LYS 373, /G LYS 373, /H LYS 373
Chain-final residues that are not actual C termini:
4217 hydrogen bonds
38136 hydrogens added
> color blue @N
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color red @O
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color atoms blue @N
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color ribbons green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> save C:/Users/zhyau/Desktop/2.cxs
——— End of log from Wed Jan 22 15:05:40 2025 ———
opened ChimeraX session
> color sel byelement
> select #1/E:<3.5 & #1/A
542 atoms, 527 bonds, 33 residues, 1 model selected
> color sel byelement
> hide H
> save C:/Users/zhyau/OneDrive/Desktop/2.cxs
> select clear
> select /A:170@NE2
1 atom, 1 residue, 1 model selected
> select clear
> select /A:170@NE2
1 atom, 1 residue, 1 model selected
> select /E:281@OH
1 atom, 1 residue, 1 model selected
> select /A:170@NE2
1 atom, 1 residue, 1 model selected
> select /E:281@OH
1 atom, 1 residue, 1 model selected
> select add /A:170@NE2
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /E:281@OH /A:170@NE2
Distance between /E TYR 281 OH and /A GLN 170 NE2: 6.194Å
> distance style decimalPlaces 4
[Repeated 2 time(s)]
> select /A:183@NZ
1 atom, 1 residue, 1 model selected
> select /A:183@NZ
1 atom, 1 residue, 1 model selected
> select /E:329@OD1
1 atom, 1 residue, 1 model selected
> select /E:329@OD1
1 atom, 1 residue, 1 model selected
> select /E:329@OD1
1 atom, 1 residue, 1 model selected
> select /A:183@NZ
1 atom, 1 residue, 1 model selected
> select add /E:329@OD1
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /A:183@NZ /E:329@OD1
Distance between /A LYS 183 NZ and /E ASP 329 OD1: 3.3356Å
> save C:/Users/zhyau/OneDrive/Desktop/2.cxs
> select /E:329@OD2
1 atom, 1 residue, 1 model selected
> select add /E:284@OH
2 atoms, 2 residues, 1 model selected
> select subtract /E:284@OH
1 atom, 1 residue, 1 model selected
> select /E:284@OH
1 atom, 1 residue, 1 model selected
> select add /E:329@OD2
2 atoms, 2 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> ui tool show Distances
> distance /E 281O &/ A:170N
Unknown command: measure distance /E 281O &/ A:170N
> distance :281@O @A:170@N
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 16 atoms and 0
measurable objects
> distance :281@O @A:170@N
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 16 atoms and 0
measurable objects
> select /E:154
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /E:294
16 atoms, 15 bonds, 1 residue, 1 model selected
> label :sel text "ID: %r, Type: %aa"
> undo
> select /E:291
24 atoms, 23 bonds, 1 residue, 1 model selected
> label :sel text "ID: %r, Type: %aa"
> label selected size 20 color yellow text "ID: %r, Type: %aa"
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label sel size 20 color yellow text "ID: %r, Type: %aa"
> save C:/Users/zhyau/OneDrive/Desktop/2.cxs
——— End of log from Wed Jan 22 22:30:09 2025 ———
opened ChimeraX session
> select /E:85
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
73 atoms, 74 bonds, 4 residues, 1 model selected
> select up
5787 atoms, 5843 bonds, 373 residues, 1 model selected
> select down
73 atoms, 74 bonds, 4 residues, 1 model selected
> select down
22 atoms, 21 bonds, 1 residue, 1 model selected
> select down
22 atoms, 21 bonds, 1 residue, 1 model selected
> select down
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B /C /D
Alignment identifier is 1
> select /A-D:1
76 atoms, 72 bonds, 4 residues, 1 model selected
> select /A-D:1-68
4020 atoms, 4088 bonds, 272 residues, 1 model selected
> select /A-D:1
76 atoms, 72 bonds, 4 residues, 1 model selected
> select /A-D:1-114
6720 atoms, 6808 bonds, 456 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain /E /F /G /H
Alignment identifier is 2
> select /E-H:1
76 atoms, 72 bonds, 4 residues, 1 model selected
> select /E-H:1-5
348 atoms, 344 bonds, 20 residues, 1 model selected
> select /E-H:1
76 atoms, 72 bonds, 4 residues, 1 model selected
> select /E-H:1-67
4060 atoms, 4108 bonds, 268 residues, 1 model selected
> select /E-H:1
76 atoms, 72 bonds, 4 residues, 1 model selected
> select /E-H:1-198
12384 atoms, 12532 bonds, 792 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /E-H:228
28 atoms, 24 bonds, 4 residues, 1 model selected
> select /E-H:228-261
1764 atoms, 1776 bonds, 136 residues, 1 model selected
> select
> /E-H:11-22,25-36,41-48,92-100,105-115,118-128,148-155,160-170,176-187,199-208,217-227
7388 atoms, 7420 bonds, 460 residues, 1 model selected
> select /E-H:217
68 atoms, 68 bonds, 4 residues, 1 model selected
> select /E-H:217-227
692 atoms, 696 bonds, 44 residues, 1 model selected
> select /E-H:199
68 atoms, 68 bonds, 4 residues, 1 model selected
> select /E-H:199-227
1832 atoms, 1848 bonds, 116 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /A:279
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> color sel byhetero
> ui tool show "Color Actions"
> color sel cadet blue
> color sel steel blue
> color sel slate gray
> color sel dark cyan
> color sel cornflower blue
> color sel medium aquamarine
[Repeated 1 time(s)]
> color sel steel blue
> color sel cadet blue
[Repeated 1 time(s)]
> color sel light slate gray
[Repeated 1 time(s)]
> color sel slate gray
[Repeated 2 time(s)]
> color sel light slate gray
> color sel medium aquamarine
> color sel teal
> color sel steel blue
[Repeated 1 time(s)]
> color sel cadet blue
> color sel light slate gray
> select clear
> select /A:277
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel light slate gray
> hide sel atoms
> select /A:227
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:320
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:321
17 atoms, 17 bonds, 1 residue, 1 model selected
> hide sel cartoons
> undo
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select /A:323
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> color sel light slate gray
> select /A:320
19 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
> select /A:321
17 atoms, 17 bonds, 1 residue, 1 model selected
> select /A:762
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:321
17 atoms, 17 bonds, 1 residue, 1 model selected
> select add /A:320
36 atoms, 35 bonds, 2 residues, 1 model selected
> color sel light slate gray
> select /A:227
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel light slate gray
> view
> save C:/Users/zhyau/OneDrive/Desktop/2.cxs
——— End of log from Thu Jan 23 11:55:14 2025 ———
opened ChimeraX session
> select /A:161
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
117 atoms, 116 bonds, 7 residues, 1 model selected
> select up
13351 atoms, 13505 bonds, 839 residues, 1 model selected
> show sel surface'
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sel surfaces
> select /A-D:1
76 atoms, 72 bonds, 4 residues, 1 model selected
> select /A-D:1-110
6416 atoms, 6500 bonds, 440 residues, 1 model selected
> select /A-D:114
48 atoms, 44 bonds, 4 residues, 1 model selected
> select /A-D:1-114
6720 atoms, 6808 bonds, 456 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> select /A:332@CG
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 1 residue, 2 models selected
> select up
131 atoms, 130 bonds, 8 residues, 2 models selected
> select up
13351 atoms, 13505 bonds, 839 residues, 2 models selected
> transparency (#!1 & sel) 80
> select clear
> select /A-D:98
44 atoms, 40 bonds, 4 residues, 1 model selected
> select /A-D:97-98
100 atoms, 96 bonds, 8 residues, 1 model selected
> select /A-D:115
96 atoms, 92 bonds, 4 residues, 1 model selected
> select /A-D:115-353
14924 atoms, 15032 bonds, 956 residues, 1 model selected
> select /A-D:115
96 atoms, 92 bonds, 4 residues, 1 model selected
> select /A-D:115-383
16936 atoms, 17084 bonds, 1076 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /E /F /G /H
Alignment identifier is 2
> select /E-H:1
76 atoms, 72 bonds, 4 residues, 1 model selected
> select /E-H:1-125
7840 atoms, 7936 bonds, 500 residues, 1 model selected
> select /E-H:154
40 atoms, 36 bonds, 4 residues, 1 model selected
> select /E-H:154-345
11696 atoms, 11792 bonds, 768 residues, 1 model selected
> select /E-H:154
40 atoms, 36 bonds, 4 residues, 1 model selected
> select /E-H:154-373
13512 atoms, 13612 bonds, 880 residues, 1 model selected
> select /A-D:675-676
152 atoms, 148 bonds, 8 residues, 1 model selected
> select /A-D:675-772
6380 atoms, 6436 bonds, 392 residues, 1 model selected
> select /A-D:647
48 atoms, 44 bonds, 4 residues, 1 model selected
> select /A-D:647-650
264 atoms, 264 bonds, 16 residues, 1 model selected
> select /A-D:839
92 atoms, 88 bonds, 4 residues, 1 model selected
> select /A-D:749-839
5700 atoms, 5764 bonds, 364 residues, 1 model selected
> select /A-D:252
56 atoms, 56 bonds, 4 residues, 1 model selected
> select /A-D:252-346
5816 atoms, 5856 bonds, 380 residues, 1 model selected
> select /A-D:367
44 atoms, 40 bonds, 4 residues, 1 model selected
> select /A-D:367-461
6308 atoms, 6404 bonds, 380 residues, 1 model selected
> select /A-D:158
44 atoms, 40 bonds, 4 residues, 1 model selected
> select /A-D:158-283
7848 atoms, 7912 bonds, 504 residues, 1 model selected
> select /A-D:1
76 atoms, 72 bonds, 4 residues, 1 model selected
> select /A-D:1-175
10588 atoms, 10696 bonds, 700 residues, 1 model selected
> save C:/Users/zhyau/OneDrive/Desktop/2.cxs
> ui tool show "Color Actions"
> ui tool show "Basic Actions"
> ui tool show "Render/Select by Attribute"
> cartoon style (#!1 & sel) xsection rectangle modeHelix default
> undo
> cartoon style (#!1 & sel) xsection oval modeHelix default
> undo
> cartoon style (#!1 & sel & coil) xsection oval
> cartoon style (#!1 & sel) xsection barbell modeHelix default
> undo
> cartoon style (#!1 & sel) modeHelix tube sides 20
> undo
> cartoon style (#!1 & sel) modeHelix tube sides 20
> undo
> show sel tube helix
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sel tube helices
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select up
11164 atoms, 11272 bonds, 732 residues, 2 models selected
> select up
53404 atoms, 54020 bonds, 3356 residues, 2 models selected
> select down
11164 atoms, 11272 bonds, 732 residues, 2 models selected
> select down
10588 atoms, 10696 bonds, 700 residues, 2 models selected
Drag select of I.cif_A SES surface, 49531 of 1181730 triangles, 63 residues
> cartoon style (#!1 & sel) modeHelix tube sides 20
> undo
> select #1/E:50-100
826 atoms, 843 bonds, 51 residues, 1 model selected
> select #1/E:152-200
758 atoms, 766 bonds, 49 residues, 1 model selected
> select #1/E:500-700
Nothing selected
> select #1/A:500-700
3299 atoms, 3338 bonds, 201 residues, 1 model selected
> cartoon style (#!1 & sel) modeHelix tube sides 20
> undo
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #1.2 models
> show #1.2 models
> hide #1.1 models
> show #1.1 models
> save C:/Users/zhyau/OneDrive/Desktop/2.cxs
——— End of log from Thu Jan 23 13:17:21 2025 ———
opened ChimeraX session
> select helix
34374 atoms, 34532 bonds, 2066 residues, 1 model selected
> select clear
> select backbone
29212 atoms, 29204 bonds, 4848 residues, 1 model selected
> select clear
> select ~sel & ##selected
Nothing selected
> select /E:295
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
162 atoms, 162 bonds, 10 residues, 1 model selected
> select up
5787 atoms, 5843 bonds, 373 residues, 1 model selected
> color sel lime
> color sel byelement
> select /A:269@O
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 2 models selected
> select up
161 atoms, 161 bonds, 9 residues, 2 models selected
> select up
13351 atoms, 13505 bonds, 839 residues, 2 models selected
> color (#!1 & sel) orange
> transparency (#!1 & sel) 80
> set bgColor white
> hide #!2 models
> hide #2.1 models
> hide #!1 models
> show #!1 models
> save C:/Users/zhyau/OneDrive/Desktop/2.cxs
——— End of log from Thu Jan 23 15:06:07 2025 ———
> view name session-start
opened ChimeraX session
OpenGL version: 3.3.0 NVIDIA 566.07
OpenGL renderer: NVIDIA GeForce RTX 4070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: zh_CN.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: ASUSTeK COMPUTER INC.
Model: ASUS TUF Gaming F15 FX507VI_FX507VI
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 16,780,505,088
MaxProcessMemory: 137,438,953,344
CPU: 16 13th Gen Intel(R) Core(TM) i7-13620H
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
anyio: 4.8.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.2.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.12.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
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: 2.17
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60
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: 1.0.2
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: 1.5.8
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202501230202
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: 1.2.7
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: 1.5.1
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: 2.7.7
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-ProfileGrids: 1.0.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.15
ChimeraX-Shape: 1.1
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: 1.19.1
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: 2.5.1
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: 1.43
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
comtypes: 1.4.5
contourpy: 1.3.1
coverage: 7.6.10
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.12
decorator: 5.1.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.15.4
fonttools: 4.55.4
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
iniconfig: 2.0.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.5
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.8
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
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
pluggy: 1.5.0
prompt_toolkit: 3.0.50
psutil: 6.0.0
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: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.1
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
pytest: 8.3.4
pytest-cov: 6.0.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.1
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: 3.10.2
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: 2025.1
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (2)
comment:1 by , 9 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → QObject::killTimer: Timers cannot be stopped from another thread |
comment:2 by , 9 months ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
The error messages indicate a PyQt object was deleted in a non-gui thread
QObject::killTimer: Timers cannot be stopped from another thread
QObject::~QObject: Timers cannot be stopped from another thread
This can easily happen when the Python garbage collector runs in a non-gui thread which is a normal behavior. Here is a Github issue for Napari that discusses this problem, and I see I commented on it a few years ago because we got Qt crashes when making the QOpenGLContext current in wrong thread.
Unfortunately we are just screwed here. I don't think there is any viable solution. PyQt and Python garbage collection simply don't work together. We know a major weakness of Python is poor multi-threading support. Garbage collection in the wrong thread can cause crashes in other things besides PyQt -- basically any library that requires creation and destruction or other operations to be done in the same thread. So OpenGL is subject to this problem.
I would like to know how many of our mystery "Qt event loop" crashes are caused by this garbage collection in the wrong thread.
To minimize the occurence of these crashes I think we should simply minimize the use of threads.
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Open to ideas about how this happens...