![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 15 months ago
#15687 closed defect (can't reproduce)
Crash floating window on Mac
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | pett | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00000001e3255ec0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 2549 in float_changed
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 56)
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"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "2106"
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"base" : 6835458048,
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"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 2883584,
"uuid" : "4dffb7eb-bbcd-3ff6-a203-5a0b97358ee8",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> help help:quickstart
> open 2bbv
Summary of feedback from opening 2bbv fetched from pdb
---
notes | Fetching compressed mmCIF 2bbv from http://files.rcsb.org/download/2bbv.cif
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif
2bbv title:
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]
Chain information for 2bbv #1
---
Chain | Description | UniProt
A B C | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 1-363
D E F | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 364-407
N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') |
Non-standard residues in 2bbv #1
---
CA — calcium ion
2bbv mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
6| crystal asymmetric unit, crystal frame
> color bychain
> open /Users/hannah.dixon/Downloads/AF-P40763-F1-model_v4.pdb
> /Users/hannah.dixon/Downloads/AF-A0A5F4CC58-F1-model_v4.pdb
Summary of feedback from opening
/Users/hannah.dixon/Downloads/AF-A0A5F4CC58-F1-model_v4.pdb
---
warning | Ignored bad PDB record found on line 38
DBREF XXXX A 1 793 UNP A0A5F4CC58 A0A5F4CC58_CANLF 1 793
AF-P40763-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for signal transducer and activator of
transcription 3 (P40763) [more info...]
Chain information for AF-P40763-F1-model_v4.pdb #2
---
Chain | Description | UniProt
A | signal transducer and activator of transcription 3 | STAT3_HUMAN 1-770
AF-A0A5F4CC58-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for signal transducer and activator of
transcription (A0A5F4CC58) [more info...]
Chain information for AF-A0A5F4CC58-F1-model_v4.pdb #3
---
Chain | Description
A | signal transducer and activator of transcription
> hide #!1 models
> show #!1 models
> hide #!1 models
> ui tool show Matchmaker
> matchmaker #2-3 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 2bbv, chain F (#1) with AF-P40763-F1-model_v4.pdb, chain A (#2),
sequence alignment score = 31.4
RMSD between 14 pruned atom pairs is 0.410 angstroms; (across all 16 pairs:
3.358)
Matchmaker 2bbv, chain F (#1) with AF-A0A5F4CC58-F1-model_v4.pdb, chain A
(#3), sequence alignment score = 31.4
RMSD between 14 pruned atom pairs is 0.416 angstroms; (across all 16 pairs:
3.350)
> color #2 #364eecff
> color #2 #4b33ecff
> color #3 #e1bbdfff
> color #3 #efc7edff
> color #3 #89ef76ff
> color #2 #7e61e7ff
> color #2 #8939e7ff
> open P40763 fromDatabase uniprot associate #2/A
Summary of feedback from opening P40763 fetched from uniprot
---
notes | Fetching compressed P40763 UniProt info from https://www.uniprot.org/uniprot/P40763.xml
Alignment identifier is P40763
Associated AF-P40763-F1-model_v4.pdb chain A to P40763 with 0 mismatches
Opened UniProt P40763
> select #2/A:580-670
725 atoms, 740 bonds, 91 residues, 1 model selected
> select #2/A:580-670
725 atoms, 740 bonds, 91 residues, 1 model selected
> select #2/A:580
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:580-670
725 atoms, 740 bonds, 91 residues, 1 model selected
> color sel red
> select add #2
6182 atoms, 6309 bonds, 770 residues, 1 model selected
> select subtract #2
Nothing selected
> select #2/A:580
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:580-671
732 atoms, 747 bonds, 92 residues, 1 model selected
> select add #2
6182 atoms, 6309 bonds, 770 residues, 1 model selected
> select subtract #2
Nothing selected
> select ligand
Nothing selected
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #3 target m
> show #2 models
> hide #2 models
> show #2 models
> select add #2
6182 atoms, 6309 bonds, 770 residues, 1 model selected
> select subtract #2
Nothing selected
> hide #3 models
> show #3 models
> select add #3
6354 atoms, 6486 bonds, 793 residues, 1 model selected
> select subtract #3
Nothing selected
> log metadata #3
Metadata for AF-A0A5F4CC58-F1-model_v4.pdb #3
---
Title | Alphafold monomer V2.0 prediction for signal transducer and activator of transcription (A0A5F4CC58)
Source (natural) | Canis lupus familiaris
> log chains #3
Chain information for AF-A0A5F4CC58-F1-model_v4.pdb #3
---
Chain | Description
A | signal transducer and activator of transcription
> ui tool show "Selection Inspector"
> select solvent
208 atoms, 208 residues, 1 model selected
> ui mousemode right label
> select
20353 atoms, 20608 bonds, 17 pseudobonds, 2771 residues, 5 models selected
> select
20353 atoms, 20608 bonds, 17 pseudobonds, 2771 residues, 5 models selected
> select subtract #1
12536 atoms, 12795 bonds, 1563 residues, 2 models selected
> select subtract #2
6354 atoms, 6486 bonds, 793 residues, 1 model selected
> select subtract #3
Nothing selected
> ui tool show "Model Loops"
> ui tool show "Blast Protein"
> ui tool show ViewDockX
No suitable models found for ViewDockX
> color #2-3 bynucleotide
> select
20353 atoms, 20608 bonds, 17 pseudobonds, 2771 residues, 5 models selected
> ui tool show AlphaFold
> hide #2 models
> select subtract #2
14171 atoms, 14299 bonds, 17 pseudobonds, 2001 residues, 4 models selected
> select subtract #1
6354 atoms, 6486 bonds, 793 residues, 1 model selected
> alphafold predict #1/A
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
> label sel attribute name
> label sel text hannah
> undo
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> sequence chain #2/A
Alignment identifier is 2/A
> ~label (#!3 & sel) residues
> show #2 models
> select subtract #1
6354 atoms, 6486 bonds, 793 residues, 1 model selected
> select
> #2/A:3-9,12-21,28-33,35-40,43-48,50-73,77-94,98-125,139-185,190-252,261-290,297-320,356-358,467-483,492-494,501-515,522-533,546-551,561-575,577-581,591-600,642-645,650-656,679-686,730-736
3206 atoms, 3245 bonds, 381 residues, 1 model selected
> select
> #2/A:321-325,338-340,347-351,363-368,384-387,391-393,405-408,412-415,439-447,450-457,462-464,606-610,619-626,632-636
610 atoms, 608 bonds, 72 residues, 1 model selected
> select
> #2/A:3-9,12-21,28-33,35-40,43-48,50-73,77-94,98-125,139-185,190-252,261-290,297-320,356-358,467-483,492-494,501-515,522-533,546-551,561-575,577-581,591-600,642-645,650-656,679-686,730-736
3206 atoms, 3245 bonds, 381 residues, 1 model selected
> select
> #2/A:321-325,338-340,347-351,363-368,384-387,391-393,405-408,412-415,439-447,450-457,462-464,606-610,619-626,632-636
610 atoms, 608 bonds, 72 residues, 1 model selected
> select
> #2/A:3-9,12-21,28-33,35-40,43-48,50-73,77-94,98-125,139-185,190-252,261-290,297-320,356-358,467-483,492-494,501-515,522-533,546-551,561-575,577-581,591-600,642-645,650-656,679-686,730-736
3206 atoms, 3245 bonds, 381 residues, 1 model selected
> ui tool show "Modeller Comparative"
> select
> #2/A:321-325,338-340,347-351,363-368,384-387,391-393,405-408,412-415,439-447,450-457,462-464,606-610,619-626,632-636
610 atoms, 608 bonds, 72 residues, 1 model selected
> select
> #2/A:3-9,12-21,28-33,35-40,43-48,50-73,77-94,98-125,139-185,190-252,261-290,297-320,356-358,467-483,492-494,501-515,522-533,546-551,561-575,577-581,591-600,642-645,650-656,679-686,730-736
3206 atoms, 3245 bonds, 381 residues, 1 model selected
> select
> #2/A:321-325,338-340,347-351,363-368,384-387,391-393,405-408,412-415,439-447,450-457,462-464,606-610,619-626,632-636
610 atoms, 608 bonds, 72 residues, 1 model selected
> select
> #2/A:3-9,12-21,28-33,35-40,43-48,50-73,77-94,98-125,139-185,190-252,261-290,297-320,356-358,467-483,492-494,501-515,522-533,546-551,561-575,577-581,591-600,642-645,650-656,679-686,730-736
3206 atoms, 3245 bonds, 381 residues, 1 model selected
> select
> #2/A:321-325,338-340,347-351,363-368,384-387,391-393,405-408,412-415,439-447,450-457,462-464,606-610,619-626,632-636
610 atoms, 608 bonds, 72 residues, 1 model selected
> sequence refseq "2/A :chain A"
Missing or invalid "refSeqInfo" argument: Expected [alignment-id:]sequence-
name-or-number or alignment-id
> select #3/A
6354 atoms, 6486 bonds, 793 residues, 1 model selected
> ui tool show "Color Actions"
> color sel bychain
> color sel byhetero
> color sel byelement
> select #2/A:467
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:467-567
811 atoms, 837 bonds, 101 residues, 1 model selected
> select #2/A:516
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:464-516
430 atoms, 445 bonds, 53 residues, 1 model selected
> color #2 #d1dae4ff
> hide #2 models
> select add #2
6182 atoms, 6309 bonds, 770 residues, 1 model selected
> show #2 models
> select subtract #2
Nothing selected
> view #2 clip false
> hide #3 target m
> show #3 target m
> hide #2 target m
> show #2 models
> view #2 clip false
> show #2 target m
> log metadata #2
Metadata for AF-P40763-F1-model_v4.pdb #2
---
Title | Alphafold monomer V2.0 prediction for signal transducer and activator of transcription 3 (P40763)
Source (natural) | Homo sapiens
> log chains #2
Chain information for AF-P40763-F1-model_v4.pdb #2
---
Chain | Description | UniProt
A | signal transducer and activator of transcription 3 | STAT3_HUMAN 1-770
> select #2/A:1-770
6182 atoms, 6309 bonds, 770 residues, 1 model selected
> open P40763 fromDatabase uniprot associate #2/A
Summary of feedback from opening P40763 fetched from uniprot
---
notes | Alignment identifier is P40763
Associated AF-P40763-F1-model_v4.pdb chain A to P40763 with 0 mismatches
Opened UniProt P40763
> select #2/A:580-670
725 atoms, 740 bonds, 91 residues, 1 model selected
> select
> #2/A:32,143,330,382,384,389,392,395,423,425,437,463,561,611,621-622,637,644,646,657-658,716
193 atoms, 179 bonds, 22 residues, 1 model selected
> select #2/A:150-162
113 atoms, 112 bonds, 13 residues, 1 model selected
> select #2/A:701,716-770
408 atoms, 413 bonds, 56 residues, 1 model selected
> select
> #2/A:321-328,338-340,345-353,363-368,373-376,384-388,391-393,404-415,439-447,450-457,461-466,514-517,557-559,605-610,619-626,632-636
809 atoms, 809 bonds, 99 residues, 1 model selected
> select #2/A:359-361,398-401,490-494,674-676
131 atoms, 132 bonds, 15 residues, 1 model selected
> select
> #2/A:321-328,338-340,345-353,363-368,373-376,384-388,391-393,404-415,439-447,450-457,461-466,514-517,557-559,605-610,619-626,632-636
809 atoms, 809 bonds, 99 residues, 1 model selected
> select #2/A:701,716-770
408 atoms, 413 bonds, 56 residues, 1 model selected
> select
> #2/A:32,143,330,382,384,389,392,395,423,425,437,463,561,611,621-622,637,644,646,657-658,716
193 atoms, 179 bonds, 22 residues, 1 model selected
> select #2/A:150-162
113 atoms, 112 bonds, 13 residues, 1 model selected
> select #2/A:701,716-770
408 atoms, 413 bonds, 56 residues, 1 model selected
> select #2/A:2,49,87,601,615,631,685,704-705,707,714,727
100 atoms, 91 bonds, 12 residues, 1 model selected
> select #2/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select
> #2/A:139-177,194-237,239-251,261-290,297-320,356-358,432-434,467-483,501-513,522-533,546-549,561-574,577-582,591-600,642-645,650-656,679-686
2114 atoms, 2135 bonds, 251 residues, 1 model selected
> select #2/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:2,49,87,601,615,631,685,704-705,707,714,727
100 atoms, 91 bonds, 12 residues, 1 model selected
> select #2/A:49,87,434-435,685,705
57 atoms, 53 bonds, 6 residues, 1 model selected
> select #2/A:133,288,460,548,652,667,730
55 atoms, 49 bonds, 7 residues, 1 model selected
> select
> #2/A:32,143,330,382,384,389,392,395,423,425,437,463,561,611,621-622,637,644,646,657-658,716
193 atoms, 179 bonds, 22 residues, 1 model selected
> open P40763 fromDatabase uniprot associate #2/A
Summary of feedback from opening P40763 fetched from uniprot
---
notes | Destroying pre-existing alignment with identifier P40763
Alignment identifier is P40763
Associated AF-P40763-F1-model_v4.pdb chain A to P40763 with 0 mismatches
Opened UniProt P40763
> select
> #2/A:139-177,194-237,239-251,261-290,297-320,356-358,432-434,467-483,501-513,522-533,546-549,561-574,577-582,591-600,642-645,650-656,679-686
2114 atoms, 2135 bonds, 251 residues, 1 model selected
> select #2/A:580-670
725 atoms, 740 bonds, 91 residues, 1 model selected
> color #2 #9fe9a8ff
> select add #2
6182 atoms, 6309 bonds, 770 residues, 1 model selected
> select subtract #2
Nothing selected
> select #2/A:580-670
725 atoms, 740 bonds, 91 residues, 1 model selected
> select #2/A:580
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:580-670
725 atoms, 740 bonds, 91 residues, 1 model selected
> select #2/A:579-580
22 atoms, 23 bonds, 2 residues, 1 model selected
> select #2/A:580-670
725 atoms, 740 bonds, 91 residues, 1 model selected
> select #2/A:579
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:579-636
464 atoms, 474 bonds, 58 residues, 1 model selected
> open P40763 fromDatabase uniprot associate #2/A
Summary of feedback from opening P40763 fetched from uniprot
---
notes | Destroying pre-existing alignment with identifier P40763
Alignment identifier is P40763
Associated AF-P40763-F1-model_v4.pdb chain A to P40763 with 0 mismatches
Opened UniProt P40763
> select #2/A:580-670
725 atoms, 740 bonds, 91 residues, 1 model selected
> select #2/A:580-670
725 atoms, 740 bonds, 91 residues, 1 model selected
> select
> #2/A:139-177,194-237,239-251,261-290,297-320,356-358,432-434,467-483,501-513,522-533,546-549,561-574,577-582,591-600,642-645,650-656,679-686
2114 atoms, 2135 bonds, 251 residues, 1 model selected
> select #2/A:2-770
6174 atoms, 6301 bonds, 769 residues, 1 model selected
> select #2/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:2,49,87,601,615,631,685,704-705,707,714,727
100 atoms, 91 bonds, 12 residues, 1 model selected
> sequence chain #3/A
Destroying pre-existing alignment with identifier 3/A
Alignment identifier is 3/A
> select #3/A:1-793
6354 atoms, 6486 bonds, 793 residues, 1 model selected
> select #3/A:1-793
6354 atoms, 6486 bonds, 793 residues, 1 model selected
> sequence chain #3/A
Destroying pre-existing alignment with identifier 3/A
Alignment identifier is 3/A
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,2
Model Number: Z14W00106LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1 (23B74)
Kernel Version: Darwin 23.1.0
Time since boot: 10 days, 7 hours, 56 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2422H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
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: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 15 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash floating window on Mac |
comment:2 by , 15 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Seems like a Qt bug. The last lines of the stack have lots of NSAccessibility calls that might be related to some operating system accessiblity preference.
Curiously the last lines of the Log before the crash say an out-of-bounds row was selected in a table. Possibly that somehow tickled a Qt bug
> sequence chain #3/A Destroying pre-existing alignment with identifier 3/A Alignment identifier is 3/A Cell requested for row 0 is out of bounds for table with 0 rows! Resizing table model.
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Happened in the Mac-specific code to make floating tools behave as full-fledged windows, specifically: