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Opened 7 weeks ago
Closed 7 weeks ago
#18680 closed defect (can't reproduce)
Crash in event loop
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.11.dev202508300055 (2025-08-30 00:55:12 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation
Current thread 0x000002e8 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "C:\Program Files\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.11.dev202508300055 (2025-08-30)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "I:\Chimera\AF Presentation\TRPV4 AF3\TRPV4 pdb data\6F55-assembly1
> SdpIIISH3 TRPV4PRD.cif\6f55-assembly1.cif" format mmcif
6f55-assembly1.cif title:
Complex structure of PACSIN SH3 domain and TRPV4 proline rich region [more
info...]
Chain information for 6f55-assembly1.cif #1
---
Chain | Description
A | PACSIN 3
B | PRR
> ui autostart false "AlphaFold Error Plot"
> ui tool show AlphaFold
> ui autostart true "AlphaFold Error Plot"
> alphafold match #1
Cannot search short sequences less than 20 amino acids
Fetching compressed AlphaFold Q1G1I6 from
https://alphafold.ebi.ac.uk/files/AF-Q1G1I6-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: Q1G1I6 (chain A)
No AlphaFold model with similar sequence for chain B
AlphaFold prediction matching 6f55-assembly1.cif
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | Q1G1I6 | Q1G1I6_CHICK | 1.44 | 64 | 67 | 98
Opened 1 AlphaFold model
> alphafold match #1/B
Cannot search short sequences less than 20 amino acids
No AlphaFold model with similar sequence for chain B
Opened 0 AlphaFold model
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> alphafold match #1/A
1 AlphaFold model found using sequence similarity searches: Q1G1I6 (chain A)
AlphaFold prediction matching 6f55-assembly1.cif
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | Q1G1I6 | Q1G1I6_CHICK | 1.44 | 64 | 67 | 98
Opened 1 AlphaFold model
> hide #2.1 models
> show #2.1 models
> hide #3.1 models
> hide #!3 models
> show #!3 models
> show #3.1 models
> hide #3.1 models
> hide #!3 models
> hide #2.1 models
> show #!3 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> hide #!3 models
> alphafold match #1/A
1 AlphaFold model found using sequence similarity searches: Q1G1I6 (chain A)
AlphaFold prediction matching 6f55-assembly1.cif
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | Q1G1I6 | Q1G1I6_CHICK | 1.44 | 64 | 67 | 98
Opened 1 AlphaFold model
> alphafold match #1/B
Cannot search short sequences less than 20 amino acids
No AlphaFold model with similar sequence for chain B
Opened 0 AlphaFold model
> close #3-4
> select add #2.1
504 atoms, 513 bonds, 64 residues, 1 model selected
> show #2.1 models
> select subtract #2.1
Nothing selected
Drag select of 8 residues
> select add #1/B:107
156 atoms, 13 bonds, 9 residues, 1 model selected
> select add #1/B:106
170 atoms, 27 bonds, 10 residues, 1 model selected
> select add #1/B:105
180 atoms, 36 bonds, 11 residues, 1 model selected
> select add #1/B:104
194 atoms, 50 bonds, 12 residues, 1 model selected
> select add #1/B:103
201 atoms, 56 bonds, 13 residues, 1 model selected
> select add #1/B:102
223 atoms, 77 bonds, 14 residues, 1 model selected
> select add #1/B:101
237 atoms, 90 bonds, 15 residues, 1 model selected
> select sequence YRQHPSENKRW
Nothing selected
> select sequence YRQHPSENKRW
Nothing selected
> select add #1
1265 atoms, 1280 bonds, 82 residues, 1 model selected
> select sequence YRQHPSENKRW
Nothing selected
> alphafold match YRQHPSENKRW
Cannot search short sequences less than 20 amino acids
No AlphaFold model with similar sequence for 1 sequences
Opened 0 AlphaFold model
> select sequence KGPAPNPPPILKV
199 atoms, 203 bonds, 13 residues, 1 model selected
> select sequence TGPAPNPPPILKV
Nothing selected
> select sequence TGPAPNPPPILKV
Nothing selected
> select sequence TKGPAPNPPPILKV
213 atoms, 217 bonds, 14 residues, 1 model selected
> select sequence KGPAPNPPPILKV
199 atoms, 203 bonds, 13 residues, 1 model selected
> select sequence TKGPAPNPPPILKVI
Nothing selected
> select sequence TKGPAPNPPPILKV
213 atoms, 217 bonds, 14 residues, 1 model selected
> select sequence TKGPAPNPPPILKVY
Nothing selected
> select sequence TKGPAPNPPPILKVU
Nothing selected
> select sequence TKGPAPNPPPILKV
213 atoms, 217 bonds, 14 residues, 1 model selected
> select sequence TKGPAPNPPPILKVW
237 atoms, 243 bonds, 15 residues, 1 model selected
> alphafold match YRQHPSENKRW
Cannot search short sequences less than 20 amino acids
No AlphaFold model with similar sequence for 1 sequences
Opened 0 AlphaFold model
> alphafold predict YRQHPSENKRW
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
> hide #1 models
> alphafold predict
> YRQHPSENKRW,IKVPGVRVRALYDYTGQEADELSFKAGEELMKISEEDEQGWCKGRLLTGHVGLYPANYVEKVGL
Running AlphaFold prediction
AlphaFold prediction finished
Results in C:\Users\RyanRechnen/Downloads/ChimeraX/AlphaFold/prediction_1
> open
> C:\Users\RyanRechnen/Downloads/ChimeraX/AlphaFold/prediction_1\best_model.pdb
Chain information for best_model.pdb #3
---
Chain | Description
A | No description available
Computing secondary structure
AlphaFold prediction finished
Results in C:\Users\RyanRechnen/Downloads/ChimeraX/AlphaFold/prediction_2
> open
> C:\Users\RyanRechnen/Downloads/ChimeraX/AlphaFold/prediction_2\best_model.pdb
Chain information for best_model.pdb #4
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> open
> C:/Users/RyanRechnen/Downloads/ChimeraX/AlphaFold/AF-A0A1D5PXA5-F1-model_v4.cif
Chain information for AF-A0A1D5PXA5-F1-model_v4.cif #5
---
Chain | Description | UniProt
A | Transient receptor potential cation channel subfamily V member 4 | TRPV4_CHICK 1-852
Color AF-A0A1D5PXA5-F1-model_v4.cif by residue attribute pLDDT_score
> open
> C:/Users/RyanRechnen/Downloads/ChimeraX/AlphaFold/AF-Q1G1I6-F1-model_v4.cif
Chain information for AF-Q1G1I6-F1-model_v4.cif #6
---
Chain | Description | UniProt
A | PACSIN 3 | Q1G1I6_CHICK 1-437
Color AF-Q1G1I6-F1-model_v4.cif by residue attribute pLDDT_score
> hide #4 models
> hide #3 models
> hide #2.1 models
> hide #!2 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie2.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie2.mp4
> hide #6 models
> show #6 models
> hide #5 models
> hide #6 models
> show #4 models
> show #3 models
> hide #4 models
> show #4 models
> show #2.1 models
> hide #2.1 models
> hide #!2 models
> show #!2 models
> select add #3
343 atoms, 353 bonds, 26 residues, 2 models selected
> select add #4
952 atoms, 975 bonds, 101 residues, 3 models selected
> select add #1
1980 atoms, 2012 bonds, 168 residues, 3 models selected
> select subtract #1
715 atoms, 732 bonds, 86 residues, 2 models selected
> view
> hide #!2 models
> show #!2 models
> show #1 models
> hide #!2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> hide #4 models
> show #4 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #3 models
> hide #4 models
> show #4 models
> show #3 models
> hide #4 models
> hide #3 models
> hide #2.1 models
> hide #!2 models
> show #2.1 models
> show #1 models
> show #3 models
> show #4 models
> matchmaker #2.1 & sel to #1 & sel
No 'to' model specified
> matchmaker #3-4#2.1 & sel to #1 & sel
No 'to' model specified
> matchmaker #3-4#2.1 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 6f55-assembly1.cif, chain B (#1) with best_model.pdb, chain A (#3),
sequence alignment score = 18.1
RMSD between 4 pruned atom pairs is 0.806 angstroms; (across all 11 pairs:
4.208)
Matchmaker 6f55-assembly1.cif, chain A (#1) with best_model.pdb, chain B (#4),
sequence alignment score = 326.2
RMSD between 58 pruned atom pairs is 0.880 angstroms; (across all 64 pairs:
1.557)
Matchmaker 6f55-assembly1.cif, chain A (#1) with AlphaFold Q1G1I6_CHICK chain
A, chain A (#2.1), sequence alignment score = 322.6
RMSD between 57 pruned atom pairs is 0.894 angstroms; (across all 64 pairs:
1.438)
> hide #!2 models
> show #!2 models
> select clear
> color #1 magenta
> color #1 #ff5500ff
> color #1 #aa00ffff
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie3.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie3.mp4
> hide #2.1 models
> hide #3 models
> hide #4 models
> hide #!2 models
> show #2.1 models
> show #3 models
> hide #3 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie4.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie4.mp4
> hide #!2 models
> hide #2.1 models
> show #3 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie5.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie5.mp4
> hide #3 models
> show #4 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie6.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie6.mp4
> open "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/nt TRPV4 bis ende PRD +
> SH3 SdpIII/tryp_chick_sh3/fold_tryp_chick_sh3_model_0.cif"
Chain information for fold_tryp_chick_sh3_model_0.cif #7
---
Chain | Description
A | .
B | .
Computing secondary structure
> alphafold pae #7 file "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/nt
> TRPV4 bis ende PRD + SH3
> SdpIII/tryp_chick_sh3\\\fold_tryp_chick_sh3_full_data_0.json"
> color bfactor #7 palette alphafold
1497 atoms, 193 residues, atom bfactor range 27.5 to 95.5
> hide #4 models
> show #4 models
> matchmaker #3-4,7#2.1 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 6f55-assembly1.cif, chain B (#1) with best_model.pdb, chain A (#3),
sequence alignment score = 18.1
RMSD between 4 pruned atom pairs is 0.806 angstroms; (across all 11 pairs:
4.208)
Matchmaker 6f55-assembly1.cif, chain A (#1) with best_model.pdb, chain B (#4),
sequence alignment score = 326.2
RMSD between 58 pruned atom pairs is 0.880 angstroms; (across all 64 pairs:
1.557)
Matchmaker 6f55-assembly1.cif, chain A (#1) with
fold_tryp_chick_sh3_model_0.cif, chain A (#7), sequence alignment score =
262.7
RMSD between 53 pruned atom pairs is 0.829 angstroms; (across all 59 pairs:
1.217)
Matchmaker 6f55-assembly1.cif, chain A (#1) with AlphaFold Q1G1I6_CHICK chain
A, chain A (#2.1), sequence alignment score = 322.6
RMSD between 57 pruned atom pairs is 0.894 angstroms; (across all 64 pairs:
1.438)
> alphafold predict
> VRVRALYDYAGQEADELSFRAGEELLKMSEEDEQGWCQGQLQSGRIGLYPANYVECVGA,MADPEDPRDAGDVLGDDSFPLSSLANLFEVEDTPSPAEPSRGPPGAVDGKQNLRMKFHGAFRKGPPKPMELLESTIYESSVVPAPKKAPMDSLFDYGTYRQHPSENKRWRRRVVEKPVAGTKGPAPNPPPILKV
Running AlphaFold prediction
> hide #4 models
> show #4 models
> hide #4 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie7.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie7.mp4
> hide #7 models
> show #4 models
> show #7 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie8.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie8.mp4
> alphafold contacts #4/A toAtoms #4/B distance 8
Structure best_model.pdb #4 does not have PAE data opened
> alphafold contacts #7/A toAtoms #7/B distance 8
Found 110 residue or atom pairs within distance 8
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> undo
> show #!7 models
> delete alphafold contacts #7/A to #7/B distance 8
Missing or invalid "atoms" argument: invalid atoms specifier
> delete contacts #7/A to #7/B distance 8
Missing or invalid "atoms" argument: invalid atoms specifier
> delete #7/A to #7/B distance 8
Expected a keyword
> delete link #7/A to #7/B distance 8
Missing or invalid "atoms" argument: invalid atoms specifier
> close #7
> open "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/nt TRPV4 bis ende PRD +
> SH3 SdpIII/tryp_chick_sh3/fold_tryp_chick_sh3_model_0.cif"
Chain information for fold_tryp_chick_sh3_model_0.cif #7
---
Chain | Description
A | .
B | .
> open "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/nt TRPV4 bis ende PRD +
> SH3 SdpIII/tryp_chick_sh3/fold_tryp_chick_sh3_model_1.cif"
Chain information for fold_tryp_chick_sh3_model_1.cif #8
---
Chain | Description
A | .
B | .
> open "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/nt TRPV4 bis ende PRD +
> SH3 SdpIII/tryp_chick_sh3/fold_tryp_chick_sh3_model_2.cif"
Chain information for fold_tryp_chick_sh3_model_2.cif #9
---
Chain | Description
A | .
B | .
> open "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/nt TRPV4 bis ende PRD +
> SH3 SdpIII/tryp_chick_sh3/fold_tryp_chick_sh3_model_3.cif"
Chain information for fold_tryp_chick_sh3_model_3.cif #10
---
Chain | Description
A | .
B | .
> open "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/nt TRPV4 bis ende PRD +
> SH3 SdpIII/tryp_chick_sh3/fold_tryp_chick_sh3_model_4.cif"
Chain information for fold_tryp_chick_sh3_model_4.cif #11
---
Chain | Description
A | .
B | .
Computing secondary structure
> close #5-6
> alphafold pae #7 file "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/nt
> TRPV4 bis ende PRD + SH3
> SdpIII/tryp_chick_sh3\\\fold_tryp_chick_sh3_full_data_0.json"
> hide #1 models
> color bfactor #7 palette alphafold
1497 atoms, 193 residues, atom bfactor range 27.5 to 95.5
> alphafold pae #8 file "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/nt
> TRPV4 bis ende PRD + SH3
> SdpIII/tryp_chick_sh3\\\fold_tryp_chick_sh3_full_data_1.json"
> alphafold pae #9 file "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/nt
> TRPV4 bis ende PRD + SH3
> SdpIII/tryp_chick_sh3\\\fold_tryp_chick_sh3_full_data_2.json"
> color bfactor #9 palette alphafold
1497 atoms, 193 residues, atom bfactor range 25.1 to 95.3
> alphafold pae #10 file "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/nt
> TRPV4 bis ende PRD + SH3
> SdpIII/tryp_chick_sh3\\\fold_tryp_chick_sh3_full_data_3.json"
> alphafold pae #11 file "I:/Chimera/AF Presentation/TRPV4 AF3/Pred AF3/nt
> TRPV4 bis ende PRD + SH3
> SdpIII/tryp_chick_sh3\\\fold_tryp_chick_sh3_full_data_4.json"
> color bfactor #11 palette alphafold
1497 atoms, 193 residues, atom bfactor range 26.8 to 95
> color bfactor #8 palette alphafold
1497 atoms, 193 residues, atom bfactor range 23.2 to 93.6
> color bfactor #9 palette alphafold
1497 atoms, 193 residues, atom bfactor range 25.1 to 95.3
> color bfactor #7 palette alphafold
1497 atoms, 193 residues, atom bfactor range 27.5 to 95.5
> color bfactor #10 palette alphafold
1497 atoms, 193 residues, atom bfactor range 29 to 94.4
> select sequence TKGPAPNPPPILKV
718 atoms, 742 bonds, 84 residues, 6 models selected
> matchmaker #3-4,7-11#2.1 & sel to #1/B & sel pairing bs
Parameters
---
Chain pairing | bs
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 6f55-assembly1.cif, chain B (#1) with
fold_tryp_chick_sh3_model_0.cif, chain B (#7), sequence alignment score = 71.4
RMSD between 6 pruned atom pairs is 0.894 angstroms; (across all 14 pairs:
8.416)
Matchmaker 6f55-assembly1.cif, chain B (#1) with
fold_tryp_chick_sh3_model_1.cif, chain B (#8), sequence alignment score = 56.4
RMSD between 9 pruned atom pairs is 1.409 angstroms; (across all 14 pairs:
4.242)
Matchmaker 6f55-assembly1.cif, chain B (#1) with
fold_tryp_chick_sh3_model_2.cif, chain B (#9), sequence alignment score = 71.4
RMSD between 7 pruned atom pairs is 0.980 angstroms; (across all 14 pairs:
3.167)
Matchmaker 6f55-assembly1.cif, chain B (#1) with
fold_tryp_chick_sh3_model_3.cif, chain B (#10), sequence alignment score =
71.4
RMSD between 5 pruned atom pairs is 1.118 angstroms; (across all 14 pairs:
4.143)
Matchmaker 6f55-assembly1.cif, chain B (#1) with
fold_tryp_chick_sh3_model_4.cif, chain B (#11), sequence alignment score =
71.4
RMSD between 7 pruned atom pairs is 1.045 angstroms; (across all 14 pairs:
3.358)
> show #!2 models
> hide #!2 models
> show #!2 models
AlphaFold prediction finished
Results in C:\Users\RyanRechnen/Downloads/ChimeraX/AlphaFold/prediction_1
> open
> C:\Users\RyanRechnen/Downloads/ChimeraX/AlphaFold/prediction_1\best_model.pdb
Chain information for best_model.pdb #5
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> show #1 models
> hide #1 models
> show #1 models
> help help:user/tools/modelpanel.html
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #4 models
> show #4 models
> show #3 models
> hide #3 models
> hide #4 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #1 models
> select sequence TKGPAPNPPPILKV
818 atoms, 846 bonds, 98 residues, 7 models selected
> show #1 models
> show #!2 models
> show #3 models
> show #4 models
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> show #11 models
> matchmaker #3-5,7-11#2.1 & sel to #1/B & sel pairing bs
Parameters
---
Chain pairing | bs
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 6f55-assembly1.cif, chain B (#1) with
fold_tryp_chick_sh3_model_0.cif, chain B (#7), sequence alignment score = 71.4
RMSD between 6 pruned atom pairs is 0.894 angstroms; (across all 14 pairs:
8.416)
Matchmaker 6f55-assembly1.cif, chain B (#1) with
fold_tryp_chick_sh3_model_1.cif, chain B (#8), sequence alignment score = 56.4
RMSD between 9 pruned atom pairs is 1.409 angstroms; (across all 14 pairs:
4.242)
Matchmaker 6f55-assembly1.cif, chain B (#1) with
fold_tryp_chick_sh3_model_2.cif, chain B (#9), sequence alignment score = 71.4
RMSD between 7 pruned atom pairs is 0.980 angstroms; (across all 14 pairs:
3.167)
Matchmaker 6f55-assembly1.cif, chain B (#1) with
fold_tryp_chick_sh3_model_3.cif, chain B (#10), sequence alignment score =
71.4
RMSD between 5 pruned atom pairs is 1.118 angstroms; (across all 14 pairs:
4.143)
Matchmaker 6f55-assembly1.cif, chain B (#1) with
fold_tryp_chick_sh3_model_4.cif, chain B (#11), sequence alignment score =
71.4
RMSD between 7 pruned atom pairs is 1.045 angstroms; (across all 14 pairs:
3.358)
Matchmaker 6f55-assembly1.cif, chain B (#1) with best_model.pdb, chain B (#5),
sequence alignment score = 71.4
RMSD between 7 pruned atom pairs is 1.123 angstroms; (across all 14 pairs:
3.177)
> hide #3 models
> hide #4 models
> hide #5 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting simple
> lighting soft
> lighting simple
> graphics silhouettes false
> lighting simple
> show sel & #1 cartoons
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> show #11 models
> show sel & #1,7-11 cartoons
> ui tool show "Model Loops"
> ui tool show "Basic Actions"
> show #7/A target c
> hide #7/A target c
> show #7/A target c
> hide #7/A target c
> show #7/A target c
> hide #7/A target c
> show #7/A target c
> ui tool show Toolbar
> ui tool show Scenes
> ui tool show "Blast Protein"
> ui autostart true "Blast Protein"
> ui favorite true "Blast Protein"
> morph #7-11
Computed 201 frame morph #6
> coordset #6 1,201
> select sequence TKGPAPNPPPILKV
919 atoms, 951 bonds, 112 residues, 8 models selected
> matchmaker #3-11#2.1 & sel to #1/B & sel pairing bs
Parameters
---
Chain pairing | bs
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 6f55-assembly1.cif, chain B (#1) with
fold_tryp_chick_sh3_model_0.cif, chain B (#7), sequence alignment score = 71.4
RMSD between 6 pruned atom pairs is 0.894 angstroms; (across all 14 pairs:
8.416)
Matchmaker 6f55-assembly1.cif, chain B (#1) with
fold_tryp_chick_sh3_model_1.cif, chain B (#8), sequence alignment score = 56.4
RMSD between 9 pruned atom pairs is 1.409 angstroms; (across all 14 pairs:
4.242)
Matchmaker 6f55-assembly1.cif, chain B (#1) with
fold_tryp_chick_sh3_model_2.cif, chain B (#9), sequence alignment score = 71.4
RMSD between 7 pruned atom pairs is 0.980 angstroms; (across all 14 pairs:
3.167)
Matchmaker 6f55-assembly1.cif, chain B (#1) with
fold_tryp_chick_sh3_model_3.cif, chain B (#10), sequence alignment score =
71.4
RMSD between 5 pruned atom pairs is 1.118 angstroms; (across all 14 pairs:
4.143)
Matchmaker 6f55-assembly1.cif, chain B (#1) with
fold_tryp_chick_sh3_model_4.cif, chain B (#11), sequence alignment score =
71.4
RMSD between 7 pruned atom pairs is 1.045 angstroms; (across all 14 pairs:
3.358)
Matchmaker 6f55-assembly1.cif, chain B (#1) with best_model.pdb, chain B (#5),
sequence alignment score = 71.4
RMSD between 7 pruned atom pairs is 1.123 angstroms; (across all 14 pairs:
3.177)
Matchmaker 6f55-assembly1.cif, chain B (#1) with Morph -
fold_tryp_chick_sh3_model_0.cif, chain B (#6), sequence alignment score = 65.4
RMSD between 7 pruned atom pairs is 1.226 angstroms; (across all 14 pairs:
2.991)
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie9.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie9.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie10.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie10.mp4
> matchmaker #3-11#2.1 & sel to #1/A & sel pairing bs
No 'to' chains specified
> select sequence VRVRALYDYAGQEADELSFRAGEELLKMSEEDEQGWCQGQLQSGRIGLYPANYVECVGA
3240 atoms, 3289 bonds, 413 residues, 7 models selected
> matchmaker #3-11#2.1 & sel to #1/A & sel pairing bs
No 'to' chains specified
> matchmaker #6/A & sel to #1/A & sel pairing ss
No 'to' chains specified
> matchmaker #6/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
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 6f55-assembly1.cif, chain A (#1) with Morph -
fold_tryp_chick_sh3_model_0.cif, chain A (#6), sequence alignment score =
255.5
RMSD between 53 pruned atom pairs is 0.796 angstroms; (across all 59 pairs:
1.499)
> save C:\Users\RyanRechnen/Desktop\image1.png supersample 3
> save C:\Users\RyanRechnen/Desktop\image2.png supersample 3
> show #5 models
> select clear
> save C:\Users\RyanRechnen/Desktop\image3.png supersample 3
> hide #5 models
> save C:\Users\RyanRechnen/Desktop\image4.png supersample 3
> save C:\Users\RyanRechnen/Desktop\image5.png supersample 3
> show #5 models
> save C:\Users\RyanRechnen/Desktop\image6.png supersample 3
> morph #5
Require at least 2 structures for morph
> alphafold contacts #6/A toAtoms #6/B distance 8
Structure Morph - fold_tryp_chick_sh3_model_0.cif #6 does not have PAE data
opened
> show #7 models
> alphafold contacts #7/A toAtoms #7/B distance 8
Found 110 residue or atom pairs within distance 8
> hide #5 models
> show #5 models
> hide #!7 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\RyanRechnen/Desktop\movie11.mp4
Movie saved to C:\Users\RyanRechnen/Desktop\movie11.mp4
> matchmaker #6/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
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 6f55-assembly1.cif, chain A (#1) with Morph -
fold_tryp_chick_sh3_model_0.cif, chain A (#6), sequence alignment score =
255.5
RMSD between 53 pruned atom pairs is 0.797 angstroms; (across all 59 pairs:
1.497)
> matchmaker #6/B to #1/B pairing ss
Parameters
---
Chain pairing | ss
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 6f55-assembly1.cif, chain B (#1) with Morph -
fold_tryp_chick_sh3_model_0.cif, chain B (#6), sequence alignment score = 71.4
RMSD between 6 pruned atom pairs is 1.397 angstroms; (across all 14 pairs:
4.150)
> matchmaker #5/B to #1/B pairing ss
Parameters
---
Chain pairing | ss
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 6f55-assembly1.cif, chain B (#1) with best_model.pdb, chain B (#5),
sequence alignment score = 71.4
RMSD between 7 pruned atom pairs is 1.123 angstroms; (across all 14 pairs:
3.177)
> matchmaker #5/B to #1/B pairing ss
Parameters
---
Chain pairing | ss
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 6f55-assembly1.cif, chain B (#1) with best_model.pdb, chain B (#5),
sequence alignment score = 71.4
RMSD between 7 pruned atom pairs is 1.123 angstroms; (across all 14 pairs:
3.177)
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #7/B #8/B #9/B #10/B #11/B #5/B #6/B
Alignment identifier is 1
> sequence chain #7/A #8/A #9/A #10/A #11/A #5/A #6/A
Alignment identifier is 2
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/B
Alignment identifier is 1/B
> sequence chain #2.1/A
Alignment identifier is 2.1/A
> sequence chain #3/A#4/A
Alignment identifier is 3
> sequence chain #4/B
Alignment identifier is 4/B
> sequence chain #7/A#8/A#9/A#10/A#11/A#5/A#6/A
Alignment identifier is 4
> sequence chain #7/B#8/B#9/B#10/B#11/B#5/B#6/B
Alignment identifier is 5
> save "I:/Chimera/AF Presentation/Sequences/TRPV4 seq_predChimeraX(Colab)"
> format fasta alignment 1
> save "I:/Chimera/AF Presentation/Sequences/SH3
> seq_predChimeraX(Colab).fasta" format fasta alignment 2
> select #7/A:1 #8/A:1 #9/A:1 #10/A:1 #11/A:1 #5/A:1 #6/A:1
49 atoms, 42 bonds, 7 residues, 7 models selected
> select #7/A #8/A #9/A #10/A #11/A #5/A #6/A
3240 atoms, 3289 bonds, 413 residues, 7 models selected
. [ID: 2] region 7 chains [1-59] RMSD: 42.713
> hide #!2 models
> hide #6 models
> select #7/A:1 #8/A:1 #9/A:1 #10/A:1 #11/A:1 #5/A:1 #6/A:1
49 atoms, 42 bonds, 7 residues, 7 models selected
> select #7/A #8/A #9/A #10/A #11/A #5/A #6/A
3240 atoms, 3289 bonds, 413 residues, 7 models selected
. [ID: 4] region 7 chains [1-59] RMSD: 42.713
> show #6 models
> hide #5 models
> show #5 models
> select #7/B:1 #8/B:1 #9/B:1 #10/B:1 #11/B:1 #5/B:1 #6/B:1
56 atoms, 49 bonds, 7 residues, 7 models selected
> select #7/B #8/B #9/B #10/B #11/B #5/B #6/B
7237 atoms, 7461 bonds, 938 residues, 7 models selected
. [ID: 1] region 7 chains [1-134] RMSD: 112.725
> select #7/A:1 #8/A:1 #9/A:1 #10/A:1 #11/A:1 #5/A:1 #6/A:1
49 atoms, 42 bonds, 7 residues, 7 models selected
> select #7/A #8/A #9/A #10/A #11/A #5/A #6/A
3240 atoms, 3289 bonds, 413 residues, 7 models selected
. [ID: 2] region 7 chains [1-59] RMSD: 42.713
> hide #5 models
> show #5 models
> hide #6 models
> show #6 models
> select #7/A:1 #8/A:1 #9/A:1 #10/A:1 #11/A:1 #5/A:1 #6/A:1
49 atoms, 42 bonds, 7 residues, 7 models selected
> select #7/A #8/A #9/A #10/A #11/A #5/A #6/A
3240 atoms, 3289 bonds, 413 residues, 7 models selected
. [ID: 4] region 7 chains [1-59] RMSD: 42.713
> hide #5 models
> show #5 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> select #7/A:2 #8/A:2 #9/A:2 #10/A:2 #11/A:2 #5/A:2 #6/A:2
77 atoms, 70 bonds, 7 residues, 7 models selected
> select #7/A:2 #8/A:2 #9/A:2 #10/A:2 #11/A:2 #5/A:2 #6/A:2
77 atoms, 70 bonds, 7 residues, 7 models selected
. [ID: 2] region 7 chains [2] RMSD: 47.597
> select #7/A:1-2 #8/A:1-2 #9/A:1-2 #10/A:1-2 #11/A:1-2 #5/A:1-2 #6/A:1-2
126 atoms, 119 bonds, 14 residues, 7 models selected
> select #7/A #8/A #9/A #10/A #11/A #5/A #6/A
3240 atoms, 3289 bonds, 413 residues, 7 models selected
. [ID: 2] region 7 chains [1-59] RMSD: 42.713
> select #7/A:25-59 #8/A:25-59 #9/A:25-59 #10/A:25-59 #11/A:25-59 #5/A:25-59
> #6/A:25-59
1889 atoms, 1917 bonds, 245 residues, 7 models selected
> select #7/A:37-59 #8/A:37-59 #9/A:37-59 #10/A:37-59 #11/A:37-59 #5/A:37-59
> #6/A:37-59
1182 atoms, 1196 bonds, 161 residues, 7 models selected
. [ID: 4] region 7 chains [37-59] RMSD: 43.695
> select #7/A:1 #8/A:1 #9/A:1 #10/A:1 #11/A:1 #5/A:1 #6/A:1
49 atoms, 42 bonds, 7 residues, 7 models selected
> select #7/A #8/A #9/A #10/A #11/A #5/A #6/A
3240 atoms, 3289 bonds, 413 residues, 7 models selected
. [ID: 4] region 7 chains [1-59] RMSD: 42.713
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.dev202508300055 (2025-08-30)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 Core Profile Context 25.8.1.250723
OpenGL renderer: AMD Radeon RX 7800 XT
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.9
Locale: de_DE.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.1
Qt platform: windows
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 137,291,546,624
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i5-10400F CPU @ 2.90GHz
OSLanguage: de-DE
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.7.2
build: 1.3.0
certifi: 2025.8.3
cftime: 1.6.4.post1
charset-normalizer: 3.4.3
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.0.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.16
ChimeraX-AtomicLibrary: 14.1.23
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
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.dev202508300055
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: 1.1.4
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: 1.7.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.17.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.5.1
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: 1.15.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.3.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
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: 1.5.2
ChimeraX-Scenes: 0.2.1
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: 2.17.2
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-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: 2.5.2
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: 1.48.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.3.2
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
colorama: 0.4.6
comm: 0.2.3
comtypes: 1.4.11
contourpy: 1.3.3
coverage: 7.10.6
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.3
debugpy: 1.8.16
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.19.1
fonttools: 4.59.2
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2025.4.15
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.7
jedi: 0.19.2
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.1
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.2
matplotlib: 3.10.5
matplotlib-inline: 0.1.7
msgpack: 1.1.1
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.4.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.1
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.1
PyQt6_sip: 13.10.2
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 311
pyzmq: 27.0.2
qtconsole: 5.6.1
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
requests: 2.32.4
roman-numerals-py: 3.1.0
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
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.2
traitlets: 5.14.3
typing_extensions: 4.15.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
Change History (2)
comment:1 by , 7 weeks ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop |
comment:2 by , 7 weeks ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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