![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 hours ago
Closed 73 minutes ago
#20375 closed defect (duplicate)
Crash in QObject::event
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | chimerax-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.7.8-x86_64-i386-64bit
ChimeraX Version: 1.12rc202605080108 (2026-05-08 01:08:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000070001c0a8000 (most recent call first):
File "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Current thread 0x00007ff847bbea00 (most recent call first):
File "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 424 in event_loop
File "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imaging, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, kiwisolver._cext, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 56)
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"procRole" : "Foreground",
"version" : 2,
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"incident" : "A6A74942-D7D8-4A3C-8CD1-D64E560002B6",
"pid" : 40817,
"cpuType" : "X86-64",
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"bug_type" : "309",
"procLaunch" : "2026-05-21 09:31:05.2819 +0100",
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"procExitAbsTime" : 148472166496220,
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"procPath" : "\/Applications\/ChimeraX-1.12-rc2026.05.08.app\/Contents\/MacOS\/ChimeraX",
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"crashReporterKey" : "AD5DAD3F-C80E-DE82-9804-D336B5F757D7",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 2936,
"sleepWakeUUID" : "814E32DB-9EC7-45D4-8753-9A1A018B007A",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4395520000
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 105fe5000-105fe7000 [ 8K] r-x\/r-x SM=COW ...acOS\/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":40817},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4395520000
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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===== Log before crash start =====
UCSF ChimeraX version: 1.12rc202605080108 (2026-05-08)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/asmaalhelal/Downloads/fold_2026_05_20_parb_4_copies/fold_2026_05_20_parb_4_copies_model_0.cif
Chain information for fold_2026_05_20_parb_4_copies_model_0.cif #1
---
Chain | Description
A B C D | .
Computing secondary structure
> open
> /Users/asmaalhelal/Downloads/fold_2026_05_20_parb_4_copies/fold_2026_05_20_parb_4_copies_model_0.cif
Chain information for fold_2026_05_20_parb_4_copies_model_0.cif #2
---
Chain | Description
A B C D | .
Computing secondary structure
> ui tool show Toolbar
> color bychain
> close #2
> interfaces ~solvent
3 buried areas: A B 1618, C D 1614, B C 383
> hbonds sel reveal true
12 hydrogen bonds found
> ui mousemode right zoom
> ui tool show Contacts
> contacts sel intraModel false intraMol false ignoreHiddenModels true reveal
> true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> hbonds sel reveal true
27 hydrogen bonds found
> open
> /Users/asmaalhelal/Downloads/ChimeraX/ParA/fold_2026_03_20_para_atp/fold_2026_03_20_para_atp_model_4.cif
Chain information for fold_2026_03_20_para_atp_model_4.cif #2
---
Chain | Description
A B | .
Computing secondary structure
> close #1
> open
> /Users/asmaalhelal/Downloads/ChimeraX/ParA/fold_2026_03_20_para_atp/fold_2026_03_20_para_atp_model_3.cif
Chain information for fold_2026_03_20_para_atp_model_3.cif #1
---
Chain | Description
A B | .
Computing secondary structure
> hide #2 models
> close #1
> open
> /Users/asmaalhelal/Downloads/ChimeraX/ParA/fold_2026_03_20_para_atp/fold_2026_03_20_para_atp_model_2.cif
Chain information for fold_2026_03_20_para_atp_model_2.cif #1
---
Chain | Description
A B | .
Computing secondary structure
> close #1
> open
> /Users/asmaalhelal/Downloads/ChimeraX/ParA/fold_2026_03_20_para_atp/fold_2026_03_20_para_atp_model_1.cif
Chain information for fold_2026_03_20_para_atp_model_1.cif #1
---
Chain | Description
A B | .
Computing secondary structure
> close #1
> open
> /Users/asmaalhelal/Downloads/ChimeraX/ParA/fold_2026_03_20_para_atp/fold_2026_03_20_para_atp_model_0.cif
Chain information for fold_2026_03_20_para_atp_model_0.cif #1
---
Chain | Description
A B | .
Computing secondary structure
> close #1
> show #2 models
> sequence chain #2/A,B
Alignment identifier is 1
> select /A-B:9
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /A-B:9
18 atoms, 16 bonds, 2 residues, 1 model selected
> color sel byelement
> style sel ball
Changed 18 atom styles
> set bgColor white
> select add #2
3356 atoms, 3404 bonds, 430 residues, 1 model selected
> select subtract #2
Nothing selected
> color bfactor #1/A palette alphafold
No atoms specified
> color bfactor #2/A palette alphafold
1647 atoms, 214 residues, atom bfactor range 36.2 to 98.7
> color #009051ff
> color #558d6fff
> color #68ad87ff
> color bfactor #2/A palette alphafold
1647 atoms, 214 residues, atom bfactor range 36.2 to 98.7
> select add #2
3356 atoms, 3404 bonds, 430 residues, 1 model selected
> color sel byelement
> select subtract #2
Nothing selected
> select /A-B:9
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /A-B:9
18 atoms, 16 bonds, 2 residues, 1 model selected
> style sel sphere
Changed 18 atom styles
> style sel ball
Changed 18 atom styles
> select add #2
3356 atoms, 3404 bonds, 430 residues, 1 model selected
> select subtract #2
Nothing selected
> open 1P94 fromDatabase pdbe_bio format mmcif
Summary of feedback from opening 1P94 fetched from pdbe_bio
---
warnings | Previously completed PDB model 1 found. Trying to extend.
Previously completed PDB model 2 found. Trying to extend.
Previously completed PDB model 3 found. Trying to extend.
Previously completed PDB model 4 found. Trying to extend.
Previously completed PDB model 5 found. Trying to extend.
6 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
subunit 1 title:
NMR Structure of ParG symmetric dimer [more info...]
Chain information for subunit 1 #1.1
---
Chain | Description
A B | plasmid partition protein ParG
Chain information for subunit 2 #1.2
---
Chain | Description
A B | plasmid partition protein ParG
Chain information for subunit 3 #1.3
---
Chain | Description
A B | plasmid partition protein ParG
Chain information for subunit 4 #1.4
---
Chain | Description
A B | plasmid partition protein ParG
Chain information for subunit 5 #1.5
---
Chain | Description
A B | plasmid partition protein ParG
Chain information for subunit 6 #1.6
---
Chain | Description
A B | plasmid partition protein ParG
Chain information for subunit 7 #1.7
---
Chain | Description
A B | plasmid partition protein ParG
Chain information for subunit 8 #1.8
---
Chain | Description
A B | plasmid partition protein ParG
Chain information for subunit 9 #1.9
---
Chain | Description
A B | plasmid partition protein ParG
Chain information for subunit 10 #1.10
---
Chain | Description
A B | plasmid partition protein ParG
Chain information for subunit 11 #1.11
---
Chain | Description
A B | plasmid partition protein ParG
Opened 1 biological assemblies for 1P94
Computing secondary structure
> close #1
> open 4E09 fromDatabase pdbe_bio format mmcif
Summary of feedback from opening 4E09 fetched from pdbe_bio
---
warning | Missing or incorrect sequence information. Inferred polymer connectivity.
4E09 bioassembly 1 title:
Structure of ParF-AMPPCP, I422 form [more info...]
Chain information for 4E09 bioassembly 1 #1
---
Chain | Description
A AA | Plasmid partitioning protein ParF
Non-standard residues in 4E09 bioassembly 1 #1
---
ACP — (ACP)
SO4 — (SO4)
4E09 bioassembly 1 mmCIF Assemblies
---
1| author_and_software_defined_assembly
Opened 1 biological assemblies for 4E09
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2 to #1
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 4E09 bioassembly 1, chain A (#1) with
fold_2026_03_20_para_atp_model_4.cif, chain A (#2), sequence alignment score =
268.1
RMSD between 145 pruned atom pairs is 1.045 angstroms; (across all 197 pairs:
2.861)
> ui mousemode right "move picked models"
> view matrix models
> #2,-0.23204,-0.38002,0.8954,29.598,0.9221,-0.379,0.078104,14.304,0.30967,0.84377,0.43836,36.586
> ui mousemode right "translate selected models"
> ui mousemode right "move picked models"
> ui mousemode right zoom
> ui tool show Matchmaker
> matchmaker #2 to #1
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 4E09 bioassembly 1, chain A (#1) with
fold_2026_03_20_para_atp_model_4.cif, chain A (#2), sequence alignment score =
268.1
RMSD between 145 pruned atom pairs is 1.045 angstroms; (across all 197 pairs:
2.861)
> hide #2 models
> show #2 models
> hide #!1 models
> select add #2
3356 atoms, 3404 bonds, 430 residues, 1 model selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select subtract #2
Nothing selected
> interfaces #2 & ~solvent
3 buried areas: A B 1273, B D 392, A C 391
> ui tool show Contacts
> contacts sel intraModel false intraMol false ignoreHiddenModels true reveal
> true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> hbonds sel reveal true
55 hydrogen bonds found
> ui mousemode right "move picked models"
> view matrix models
> #2,-0.23204,-0.38002,0.8954,31.04,0.9221,-0.379,0.078104,17.644,0.30967,0.84377,0.43836,41.227
> show #!1 models
> hide #!1 models
> select subtract #3
184 atoms, 23 residues, 1 model selected
> select add #2
3356 atoms, 3404 bonds, 36 pseudobonds, 430 residues, 2 models selected
> select subtract #2
Nothing selected
> ui mousemode right select
> select clear
> select #2/A:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel
> select clear
> select #2/A:110
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel
> select #2/A:139
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel
> select clear
> hide sel
> select #2/A:199
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel
> select #2/A:186
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel
> select #2/A:145
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel
> select #2/A:140
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:176
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel
> select #2/A:177
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel
> select #2/A:178
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel
> select #2/A:38
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel
> select #2/A:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel
> select #2/A:183
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel
> select #2/A:116
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel
> select #2/A:112
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel
> select #2/A:152
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel
> select #2/A:12
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel
> ui mousemode right zoom
> hide #3 models
> hide #4 models
> show #!1 models
> hide #2 models
> show #2 models
> ui tool show Matchmaker
> matchmaker #2 to #1
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 4E09 bioassembly 1, chain A (#1) with
fold_2026_03_20_para_atp_model_4.cif, chain A (#2), sequence alignment score =
268.1
RMSD between 145 pruned atom pairs is 1.045 angstroms; (across all 197 pairs:
2.861)
> hide #!1 models
> show #!1 models
> style sphere
Changed 6490 atom styles
> select #1/A:1-206
1531 atoms, 1549 bonds, 1 pseudobond, 204 residues, 2 models selected
> hide sel cartoons
> select #2/A:1-214
1647 atoms, 1669 bonds, 27 pseudobonds, 214 residues, 2 models selected
> hide sel cartoons
> style sel stick
Changed 1647 atom styles
> style sel sphere
Changed 1647 atom styles
> select subtract #3
1647 atoms, 1669 bonds, 27 pseudobonds, 214 residues, 2 models selected
> select add #4
1647 atoms, 1669 bonds, 55 pseudobonds, 214 residues, 2 models selected
> select add #2
3356 atoms, 3404 bonds, 55 pseudobonds, 430 residues, 2 models selected
> select subtract #4
3356 atoms, 3404 bonds, 430 residues, 1 model selected
> select subtract #3
3356 atoms, 3404 bonds, 430 residues, 1 model selected
> select subtract #2
Nothing selected
> style stick
Changed 6490 atom styles
> select #1.11/A:1-76
Nothing selected
> select #1.11/B:1-76
Nothing selected
> select #1.11/A:1-76
Nothing selected
> select #1/A:1-206
1531 atoms, 1549 bonds, 1 pseudobond, 204 residues, 2 models selected
> hide sel atoms
> select #1/A:1-214
1531 atoms, 1549 bonds, 1 pseudobond, 204 residues, 2 models selected
> select #1/A:1-214
1531 atoms, 1549 bonds, 1 pseudobond, 204 residues, 2 models selected
> select #1/B:1-214
Nothing selected
> select #1/A:1-214
1531 atoms, 1549 bonds, 1 pseudobond, 204 residues, 2 models selected
> select #2/A:1-214
1647 atoms, 1669 bonds, 27 pseudobonds, 214 residues, 2 models selected
> hide sel atoms
> hide #2 models
> select #1.4/A:1-76
Nothing selected
> select #2/A:1-214
1647 atoms, 1669 bonds, 27 pseudobonds, 214 residues, 2 models selected
> show #2 models
> hide #!1 models
> select #2/B:1-214
1647 atoms, 1669 bonds, 214 residues, 1 model selected
> select #2/B:1-214
1647 atoms, 1669 bonds, 214 residues, 1 model selected
> select #2/A:1-214
1647 atoms, 1669 bonds, 27 pseudobonds, 214 residues, 2 models selected
> show sel cartoons
> show sel atoms
> hide sel atoms
> select #1/A:1-206
1531 atoms, 1549 bonds, 1 pseudobond, 204 residues, 2 models selected
> select #1/A:1-206
1531 atoms, 1549 bonds, 1 pseudobond, 204 residues, 2 models selected
> select #1/A:1-206
1531 atoms, 1549 bonds, 1 pseudobond, 204 residues, 2 models selected
> select #2/A:1-214
1647 atoms, 1669 bonds, 27 pseudobonds, 214 residues, 2 models selected
> select add #2
3356 atoms, 3404 bonds, 36 pseudobonds, 430 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> show sel atoms
> show sel cartoons
> hide sel atoms
> select subtract #3
3356 atoms, 3404 bonds, 36 pseudobonds, 430 residues, 2 models selected
> select add #4
3356 atoms, 3404 bonds, 55 pseudobonds, 430 residues, 2 models selected
> select subtract #4
3356 atoms, 3404 bonds, 430 residues, 1 model selected
> select subtract #3
3356 atoms, 3404 bonds, 430 residues, 1 model selected
> select #2/A-B:9
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A-B:9
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #2
3356 atoms, 3404 bonds, 36 pseudobonds, 430 residues, 2 models selected
> select #2/A:1-214
1647 atoms, 1669 bonds, 27 pseudobonds, 214 residues, 2 models selected
> select #2/A:1-214
1647 atoms, 1669 bonds, 27 pseudobonds, 214 residues, 2 models selected
> select add #2
3356 atoms, 3404 bonds, 36 pseudobonds, 430 residues, 2 models selected
> select subtract #2
Nothing selected
> ui mousemode right "move label"
> select add #2
3356 atoms, 3404 bonds, 36 pseudobonds, 430 residues, 2 models selected
> select subtract #3
3356 atoms, 3404 bonds, 36 pseudobonds, 430 residues, 2 models selected
> select add #4
3356 atoms, 3404 bonds, 55 pseudobonds, 430 residues, 2 models selected
> ui mousemode right "move label"
> ui mousemode right label
> ui mousemode right "move label"
> select ::name="ATP"
62 atoms, 66 bonds, 2 residues, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> select add #2
3356 atoms, 3404 bonds, 36 pseudobonds, 430 residues, 2 models selected
> select subtract #2
Nothing selected
> select #2/A-B:9
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A-B:9
18 atoms, 16 bonds, 2 residues, 1 model selected
> hide sel atoms
> style sel ball
Changed 18 atom styles
> show sel atoms
> select add #2
3356 atoms, 3404 bonds, 36 pseudobonds, 430 residues, 2 models selected
> select subtract #2
Nothing selected
> ui mousemode right "move picked models"
> view matrix models
> #2,-0.23204,-0.38002,0.8954,35.891,0.9221,-0.379,0.078104,17.698,0.30967,0.84377,0.43836,47.328
> ui mousemode right zoom
> ui mousemode right "move picked models"
> view matrix models
> #2,-0.23204,-0.38002,0.8954,40.469,0.9221,-0.379,0.078104,17.016,0.30967,0.84377,0.43836,45.08
> hide #2 models
> show #!1 models
> select add #1
3134 atoms, 3172 bonds, 2 pseudobonds, 412 residues, 2 models selected
> show sel cartoons
> select subtract #1
Nothing selected
> view matrix models #1,1,0,0,1.5535,0,1,0,2.1295,0,0,1,-1.3126
> show #2 models
> hide #2/A
> select #2/A
1647 atoms, 1669 bonds, 27 pseudobonds, 214 residues, 2 models selected
> hide sel cartoons
> select #1/A
1531 atoms, 1549 bonds, 1 pseudobond, 204 residues, 2 models selected
> hide sel cartoons
> select ::name="ACP"
62 atoms, 66 bonds, 2 residues, 1 model selected
> select add #1
3134 atoms, 3172 bonds, 2 pseudobonds, 412 residues, 2 models selected
> select subtract #1
Nothing selected
> select :ACP
62 atoms, 66 bonds, 2 residues, 1 model selected
> select :ACP
62 atoms, 66 bonds, 2 residues, 1 model selected
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.12rc202605080108 (2026-05-08)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.7.3
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.
Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro14,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 529.140.2.0.0
OS Loader Version: 577.140.2~30
SMC Version (system): 2.43f11
Software:
System Software Overview:
System Version: macOS 13.7.8 (22H730)
Kernel Version: Darwin 22.6.0
Time since boot: 3 days, 7 hours, 12 minutes
Graphics/Displays:
Intel Iris Plus Graphics 640:
Chipset Model: Intel Iris Plus Graphics 640
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5926
Revision ID: 0x0006
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.2.0
bs4: 0.0.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12rc202605080108
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.1
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
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-MatchAlign: 1.1
ChimeraX-MatchMaker: 2.4
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.8
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
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: 1.0.1
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: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
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: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.6
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.3
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.5
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.20
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.62.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.13
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.20.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.9.6
plotly: 6.7.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.4
pydantic-settings: 2.14.0
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.17.1
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.10.2
PyQt6-Qt6: 6.10.1
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.1
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.27
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
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
sse-starlette: 3.4.2
stack-data: 0.6.3
starlette: 1.0.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.5
tqdm: 4.67.3
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.46.0
wcwidth: 0.7.0
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.23.0
Change History (2)
comment:1 by , 82 minutes ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in QObject::event |
comment:2 by , 73 minutes ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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