id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15687	Crash floating window on Mac	chimerax-bug-report@…	Tom Goddard	"{{{
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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===== 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
}}}
"	defect	closed	normal		Window Toolkit		can't reproduce		Eric Pettersen				all	ChimeraX