![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Last modified 15 months ago
#15642 assigned defect
MD Viewer: 'close' during playback produce traceback
| Reported by: | Owned by: | Kyle Diller | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.3.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/justinlee/code/oROS-HT_revision/halo5rerun2.cxs format session
Log from Thu Jul 18 12:44:03 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/justinlee/Documents/Research/Protein/Structures/ChimeraX_sessions/haloalign_oxyr_halocamp.cxs
Log from Tue Nov 9 19:39:02 2021UCSF ChimeraX version: 1.2.1 (2021-05-05)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/justinlee/Desktop/ROSpaperprep2021/halodimer.cxs
Log from Sat Nov 6 18:25:22 2021UCSF ChimeraX version: 1.2.1 (2021-05-05)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/justinlee/Downloads/AlphaFold
> Predictions/dimerHalo5_model_3_ptm_seed_0_unrelaxed.pdb" format pdb
Chain information for dimerHalo5_model_3_ptm_seed_0_unrelaxed.pdb #1
---
Chain | Description
A B | No description available
> open "/Users/justinlee/Downloads/AlphaFold
> Predictions/Halo5_rank_1_model_3_ptm_seed_0_unrelaxed.pdb"
Chain information for Halo5_rank_1_model_3_ptm_seed_0_unrelaxed.pdb #2
---
Chain | Description
A | No description available
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker dimerHalo5_model_3_ptm_seed_0_unrelaxed.pdb, chain B (#1) with
Halo5_rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#2), sequence
alignment score = 2857.5
RMSD between 518 pruned atom pairs is 0.581 angstroms; (across all 547 pairs:
1.428)
> open 6U2M
6u2m title:
Crystal structure of a HaloTag-based calcium indicator, HaloCaMP V2, bound to
JF635 [more info...]
Chain information for 6u2m #3
---
Chain | Description
A C | HaloCaMP V2
Non-standard residues in 6u2m #3
---
CA — calcium ion
CL — chloride ion
PUJ —
(1E,3S)-1-{10-[2-carboxy-5-({2-[2-(hexyloxy)ethoxy]ethyl}carbamoyl)phenyl]-7-(3-fluoroazetidin-1-yl)-5,5-dimethyldibenz
o[b,e]silin-3(5H)-ylidene}-3-fluoroazetidin-1-ium (JF635)
6u2m mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> matchmaker #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 dimerHalo5_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#1) with
6u2m, chain C (#3), sequence alignment score = 1618.9
RMSD between 281 pruned atom pairs is 0.431 angstroms; (across all 383 pairs:
15.057)
> matchmaker #3 to #1/B
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 dimerHalo5_model_3_ptm_seed_0_unrelaxed.pdb, chain B (#1) with
6u2m, chain C (#3), sequence alignment score = 1618.9
RMSD between 281 pruned atom pairs is 0.437 angstroms; (across all 383 pairs:
15.087)
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /B:1-547
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select #2/A:1-547
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> select #2/A:1-547
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> select #2/A:1-547
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /B:1-547
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> select /B:1-547
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> select /B:1-547
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> ~select #2
7980 atoms, 8197 bonds, 1 pseudobond, 1011 residues, 3 models selected
> select #1
8540 atoms, 8780 bonds, 1094 residues, 1 model selected
> ~select #1
Nothing selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select #3/C:4-489
3710 atoms, 3807 bonds, 1 pseudobond, 464 residues, 2 models selected
> select #3/A:4-489
3710 atoms, 3807 bonds, 1 pseudobond, 464 residues, 2 models selected
> hide sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> hide sel cartoons
> ui mousemode right select
Drag select of 22 residues, 59 atoms, 4 pseudobonds, 55 bonds
Drag select of 59 atoms, 4 pseudobonds, 55 bonds
> show sel atoms
> hide sel atoms
> select /B:1-547
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> ~select #2
7980 atoms, 8197 bonds, 1 pseudobond, 1011 residues, 3 models selected
> select #3
7733 atoms, 7724 bonds, 58 pseudobonds, 1143 residues, 3 models selected
> select #1
8540 atoms, 8780 bonds, 1094 residues, 1 model selected
> ~select #1
Nothing selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /B:1-547
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> select /B:1-547
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
Alignment identifier is 1
Alignment identifier is 3/A
> select #1/A:504-547 #2/A:504-547
714 atoms, 728 bonds, 88 residues, 2 models selected
> select #1/A:1-547 #2/A:1-547
8540 atoms, 8780 bonds, 1094 residues, 2 models selected
Seqview [ID: 1] region 2 chains [1-547] RMSD: 59.810
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> show sel atoms
> hide sel atoms
> select clear
Drag select of 299 residues
> select #1/A:1 #2/A:1
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/A:1-547 #2/A:1-547
8540 atoms, 8780 bonds, 1094 residues, 2 models selected
Seqview [ID: 1] region 2 chains [1-547] RMSD: 59.810
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> select /B:1-547
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> select /B:1-547
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> hide ribbons #1/B
Expected ',' or a keyword
> hide ribbons #1
Expected ',' or a keyword
> hide #1/B
> hide #1/B ribbons
> show #1/B ribbons
> show #1/A ribbons
> hide #1/A ribbons
> select #3/A:347-348
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #3/A:347-432
678 atoms, 685 bonds, 86 residues, 1 model selected
> select #3/A:344-345
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/A:344-489
1151 atoms, 1163 bonds, 146 residues, 1 model selected
> hide sel cartoons
> hide sel cartoons
> select #3/A:4-29
215 atoms, 220 bonds, 26 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #3/C:4-489
3710 atoms, 3807 bonds, 1 pseudobond, 464 residues, 2 models selected
Alignment identifier is 3/C
> select #3/C:4-114
917 atoms, 943 bonds, 111 residues, 1 model selected
> select #3/C:4-29
215 atoms, 220 bonds, 26 residues, 1 model selected
> hide sel cartoons
> select #3/C:344-489
1151 atoms, 1163 bonds, 146 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #3/C:4-433
3269 atoms, 3361 bonds, 1 pseudobond, 408 residues, 2 models selected
> select #3/C:4-489
3710 atoms, 3807 bonds, 1 pseudobond, 464 residues, 2 models selected
> select #3/C:4-489
3710 atoms, 3807 bonds, 1 pseudobond, 464 residues, 2 models selected
> show sel cartoons
> select /B:1-547
4270 atoms, 4390 bonds, 547 residues, 1 model selected
Alignment identifier is 1/B
> select #1/B:161
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:77-161
673 atoms, 687 bonds, 85 residues, 1 model selected
> select #1/B:123
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/B:123-129
56 atoms, 56 bonds, 7 residues, 1 model selected
> select #1/B:134
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/B:134
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/B:133-134
9 atoms, 8 bonds, 2 residues, 1 model selected
> select #1/B:131-134
29 atoms, 29 bonds, 4 residues, 1 model selected
> select #1/B:131-132
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/B:131-137
48 atoms, 48 bonds, 7 residues, 1 model selected
> show sel atoms
> select #1/B:131
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:131
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:137
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:50
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:138
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B:139
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B:132
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:132
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:131-132
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/B:131-132
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/B:131
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:131
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #1 models
> hide #!3 models
> show #2 models
> hide #2 models
> select /B:1-547
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> select /A:1-547
12250 atoms, 12587 bonds, 1 pseudobond, 1558 residues, 4 models selected
> show sel & #1 cartoons
> open 1i69
1i69 title:
Crystal structure of the reduced form of oxyr [more info...]
Chain information for 1i69 #4
---
Chain | Description
A B | hydrogen peroxide-inducible genes activator
Non-standard residues in 1i69 #4
---
BEZ — benzoic acid
> matchmaker #4 to #1/A
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 dimerHalo5_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#1) with
1i69, chain A (#4), sequence alignment score = 671.5
RMSD between 188 pruned atom pairs is 0.737 angstroms; (across all 206 pairs:
1.574)
> hide #!4 models
> hide #1 models
> show #2 models
> show #!3 models
> show #1 models
> hide #2 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #2 models
> show #!3 models
> hide #2 models
> save /Users/justinlee/Desktop/ROSpaperprep2021/halodimer.cxs
——— End of log from Sat Nov 6 18:25:22 2021 ———
opened ChimeraX session
> show #!4 models
> select #1/A
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> select #1/B
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> select #1/A
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> hide sel cartoons
> select #4/A
1626 atoms, 1666 bonds, 1 pseudobond, 207 residues, 2 models selected
> delete #4/A
> matchmaker #4 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 dimerHalo5_model_3_ptm_seed_0_unrelaxed.pdb, chain B (#1) with
1i69, chain B (#4), sequence alignment score = 678.1
RMSD between 194 pruned atom pairs is 0.721 angstroms; (across all 206 pairs:
1.634)
> select #3/C:4-29
215 atoms, 220 bonds, 26 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #3/C:344
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:344-489
1151 atoms, 1163 bonds, 146 residues, 1 model selected
> hide sel cartoons
> ui mousemode right select
Drag select of 3 atoms, 2 pseudobonds
Drag select of 4 atoms, 2 pseudobonds
> hide sel atoms
Drag select of 2 atoms, 1 pseudobonds
> hide sel atoms
> select #3/C:605@CA
1 atom, 1 residue, 1 model selected
> select add #3/C:769@O
2 atoms, 2 residues, 1 model selected
> hide sel atoms
> select #3/C:601@CL
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3
7733 atoms, 7724 bonds, 58 pseudobonds, 1143 residues, 3 models selected
> ~select #3
Nothing selected
> select #3
7733 atoms, 7724 bonds, 58 pseudobonds, 1143 residues, 3 models selected
> select clear
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> select clear
> select #1
8540 atoms, 8780 bonds, 1094 residues, 1 model selected
> color sel cornflower blue
> select clear
> save /Users/justinlee/Desktop/haloalign_oxyr_halocamp.cxs
——— End of log from Tue Nov 9 19:39:02 2021 ———
opened ChimeraX session
> show #2 models
> hide #2 models
> show #2 models
> open "/Users/justinlee/Library/CloudStorage/SynologyDrive-BerndtLab/Student
> Data/Justin
> Lee/Archive_BerndtLab/Halo5_AF3_results/JL/fold_2024_07_16_12_08/fold_2024_07_16_12_08_model_0.pdb"
Chain information for fold_2024_07_16_12_08_model_0.pdb #5
---
Chain | Description
A | No description available
> matchmaker #5 to #2
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 Halo5_rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#2) with
fold_2024_07_16_12_08_model_0.pdb, chain A (#5), sequence alignment score =
2831.7
RMSD between 269 pruned atom pairs is 0.381 angstroms; (across all 547 pairs:
15.953)
> select add #2
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #2
4270 atoms, 4390 bonds, 547 residues, 1 model selected
Alignment identifier is 2/A
> select #2/A:1-2
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:1-545
4258 atoms, 4378 bonds, 545 residues, 1 model selected
> select #2/A:547
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> open
> /Users/justinlee/Downloads/20240716_Halo5rerun_d996e_unrelaxed_alphafold2_ptm_model_1_seed_000.pdb
Chain information for
20240716_Halo5rerun_d996e_unrelaxed_alphafold2_ptm_model_1_seed_000.pdb #6
---
Chain | Description
A | No description available
> matchmaker #6 to #2
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 Halo5_rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#2) with
20240716_Halo5rerun_d996e_unrelaxed_alphafold2_ptm_model_1_seed_000.pdb, chain
A (#6), sequence alignment score = 2888.1
RMSD between 521 pruned atom pairs is 0.450 angstroms; (across all 547 pairs:
2.020)
> open
> /Users/justinlee/Downloads/20240716_Halo5rerun_d996e/20240716_Halo5rerun_d996e_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
Chain information for
20240716_Halo5rerun_d996e_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#7
---
Chain | Description
A | No description available
> open
> /Users/justinlee/Downloads/20240716_Halo5rerun_d996e/20240716_Halo5rerun_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
Chain information for
20240716_Halo5rerun_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#8
---
Chain | Description
A | No description available
> open
> /Users/justinlee/Downloads/20240716_Halo5rerun_d996e/20240716_Halo5rerun_d996e_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000.pdb
Chain information for
20240716_Halo5rerun_d996e_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000.pdb
#9
---
Chain | Description
A | No description available
> open
> /Users/justinlee/Downloads/20240716_Halo5rerun_d996e/20240716_Halo5rerun_d996e_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000.pdb
Chain information for
20240716_Halo5rerun_d996e_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000.pdb
#10
---
Chain | Description
A | No description available
> open
> /Users/justinlee/Downloads/20240716_Halo5rerun_d996e/20240716_Halo5rerun_d996e_unrelaxed_rank_004_alphafold2_ptm_model_4_seed_000.pdb
Chain information for
20240716_Halo5rerun_d996e_unrelaxed_rank_004_alphafold2_ptm_model_4_seed_000.pdb
#11
---
Chain | Description
A | No description available
> open
> /Users/justinlee/Downloads/20240716_Halo5rerun_d996e/20240716_Halo5rerun_d996e_unrelaxed_rank_005_alphafold2_ptm_model_2_seed_000.pdb
Chain information for
20240716_Halo5rerun_d996e_unrelaxed_rank_005_alphafold2_ptm_model_2_seed_000.pdb
#12
---
Chain | Description
A | No description available
> matchmaker #7 to #2
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 Halo5_rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#2) with
20240716_Halo5rerun_d996e_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#7), sequence alignment score = 2850.3
RMSD between 525 pruned atom pairs is 0.388 angstroms; (across all 547 pairs:
1.369)
> matchmaker #8 to #2
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 Halo5_rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#2) with
20240716_Halo5rerun_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#8), sequence alignment score = 2874.9
RMSD between 525 pruned atom pairs is 0.381 angstroms; (across all 547 pairs:
1.363)
> matchmaker #9 to #2
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 Halo5_rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#2) with
20240716_Halo5rerun_d996e_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000.pdb,
chain A (#9), sequence alignment score = 2861.1
RMSD between 506 pruned atom pairs is 1.076 angstroms; (across all 547 pairs:
1.579)
> matchmaker #10 to #2
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 Halo5_rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#2) with
20240716_Halo5rerun_d996e_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#10), sequence alignment score = 2888.1
RMSD between 521 pruned atom pairs is 0.450 angstroms; (across all 547 pairs:
2.020)
> matchmaker #11 to #2
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 Halo5_rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#2) with
20240716_Halo5rerun_d996e_unrelaxed_rank_004_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#11), sequence alignment score = 2859.3
RMSD between 222 pruned atom pairs is 0.194 angstroms; (across all 547 pairs:
8.914)
> matchmaker #12 to #2
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 Halo5_rank_1_model_3_ptm_seed_0_unrelaxed.pdb, chain A (#2) with
20240716_Halo5rerun_d996e_unrelaxed_rank_005_alphafold2_ptm_model_2_seed_000.pdb,
chain A (#12), sequence alignment score = 2866.5
RMSD between 219 pruned atom pairs is 0.232 angstroms; (across all 547 pairs:
10.421)
> hide #12 models
> hide #11 models
> hide #10 models
> hide #9 models
> hide #8 models
> hide #6 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> hide #5 models
> show #12 models
> hide #12 models
> show #12 models
> save /Users/justinlee/code/oROS-HT_revision/halo5rerun.cxs
> hide #7 models
> hide #12 models
> hide #10 models
> hide #9 models
> hide #11 models
> select subtract #2
Nothing selected
> show #6 models
> hide #6 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> show #11 models
> hide #11 models
> show #12 models
> hide #12 models
> show #11 models
> show #12 models
> hide #12 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #12 models
> hide #12 models
> hide #!4 models
> show #!4 models
> hide #10 models
> hide #9 models
> hide #8 models
> hide #7 models
> hide #1 models
> hide #2 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #12 models
> hide #12 models
> show #12 models
> show #11 models
> show #10 models
> show #9 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> hide #12 models
> hide #11 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> hide #9 models
> hide #10 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> hide #7 models
> hide #6 models
> hide #8 models
> hide #9 models
> show #6 models
> show #6#!3 surfaces
> hide #!3,6 surfaces
> hide #!3 models
> show #!6 surfaces
> show #!3 models
> show #7 models
> show #8 models
> hide #7 models
> show #7 models
> show #7-8#!3,6 surfaces
> show #9 models
> show #9#!3,6-8 surfaces
> show #12 models
> show #12#!3,6-9 surfaces
> hide #!12 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!6 models
> hide #!7 models
> hide #!3 models
> show #!3 models
> select add #3
7733 atoms, 7724 bonds, 58 pseudobonds, 1143 residues, 3 models selected
> hide sel surfaces
> hide sel cartoons
> color sel magenta
Alignment identifier is 1
> select #3/A-C:5
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/A-C:5-145
2274 atoms, 2344 bonds, 282 residues, 1 model selected
> select #3/A-C:147
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #3/A-C:147-327
2516 atoms, 2594 bonds, 2 pseudobonds, 318 residues, 2 models selected
> select
> #3/A-C:6-20,31-46,49-54,56-60,65-92,98-115,131-142,156-176,242-247,249-254,278-293,304-317,347-362,370-381,386-396,407-420,424-435,443-454,459-471,480-489
4324 atoms, 4388 bonds, 526 residues, 1 model selected
> select add #6
8594 atoms, 8778 bonds, 1073 residues, 4 models selected
> select subtract #6
4324 atoms, 4388 bonds, 526 residues, 4 models selected
> select add #6
8594 atoms, 8778 bonds, 1073 residues, 4 models selected
> select add #3
12003 atoms, 12114 bonds, 58 pseudobonds, 1690 residues, 7 models selected
> select subtract #3
4270 atoms, 4390 bonds, 547 residues, 4 models selected
> select add #3
12003 atoms, 12114 bonds, 58 pseudobonds, 1690 residues, 5 models selected
> select subtract #3
4270 atoms, 4390 bonds, 547 residues, 4 models selected
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> ui mousemode right select
> select clear
> select add #6
4270 atoms, 4390 bonds, 547 residues, 1 model selected
Alignment identifier is 6/A
> select #6/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:1-135
1050 atoms, 1076 bonds, 135 residues, 1 model selected
> color sel baige
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel baige
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel baige
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel beige
> hide sel surfaces
> show sel surfaces
> color sel moccasin
> select #6/A:547
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #6/A:523-547
206 atoms, 208 bonds, 25 residues, 1 model selected
> select #6/A:523-547
206 atoms, 208 bonds, 25 residues, 1 model selected
> select #6/A:456-547
722 atoms, 736 bonds, 92 residues, 1 model selected
> color sel moccasin
> select #6/A:454-455
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #6/A:451-455
40 atoms, 40 bonds, 5 residues, 1 model selected
> select #6/A:190@CG
1 atom, 1 residue, 1 model selected
> select clear
> lighting flat
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
Drag select of
20240716_Halo5rerun_d996e_unrelaxed_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface, 467 of 446860 triangles, 2 atoms, 1 bonds, 2 residues
> select clear
[Repeated 1 time(s)]
> select #3/A-C:4-271
3904 atoms, 4022 bonds, 2 pseudobonds, 492 residues, 2 models selected
> select #3/A-C:454-455
24 atoms, 22 bonds, 4 residues, 1 model selected
> select #3/A-C:38-455
6304 atoms, 6478 bonds, 2 pseudobonds, 792 residues, 2 models selected
> select #3/A-C:446-489
706 atoms, 710 bonds, 88 residues, 1 model selected
> select #3/A-C:38-489
6850 atoms, 7028 bonds, 2 pseudobonds, 860 residues, 2 models selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> ui mousemode right select
> ui mousemode right translate
> show #!8 models
> hide #!6 models
> show #10 models
> hide #!8 models
> show #!9 models
> hide #10 models
> show #10 models
> hide #!9 models
> show #10#!3 surfaces
> show #!3,10 surfaces
> hide #!3 models
> show #!3 models
> select add #3
7733 atoms, 7724 bonds, 58 pseudobonds, 1143 residues, 3 models selected
> hide sel surfaces
> show #11 models
> hide #!10 models
> show #!12 models
> hide #!12 models
> hide #11 models
> select add #11
12003 atoms, 12114 bonds, 58 pseudobonds, 1690 residues, 6 models selected
> ui mousemode right select
> select clear
Drag select of 4 atoms, 4 bonds
Drag select of 7 atoms, 6 bonds
> hide sel atoms
> show #!6 models
> hide #!6 models
> show #!12 models
> show #11 models
> hide #!12 models
> hide #11 models
> show #!12 models
> show #11 models
> hide #!12 models
> select add #11
4277 atoms, 4396 bonds, 548 residues, 3 models selected
> select add #3
12003 atoms, 12114 bonds, 58 pseudobonds, 1690 residues, 5 models selected
> select subtract #3
4270 atoms, 4390 bonds, 547 residues, 3 models selected
> show sel surfaces
[Repeated 1 time(s)]
> select subtract #11
1 model selected
> hide #!11 models
> show #!6 models
> select clear
> ui mousemode right translate
> ui mousemode right select
Drag select of
20240716_Halo5rerun_d996e_unrelaxed_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface, 35073 of 446860 triangles, 56 residues
Drag select of
20240716_Halo5rerun_d996e_unrelaxed_alphafold2_ptm_model_1_seed_000.pdb_A SES
surface, 82074 of 446860 triangles, 112 residues
> select clear
> ui mousemode right translate
> toolshed show
Downloading bundle
ChimeraX_ISOLDE-1.7.1-cp311-cp311-macosx_10_13_universal2.whl
> ui tool show "Measure Volume and Area"
> save /Users/justinlee/code/oROS-HT_revision/halo5rerun2.cxs
——— End of log from Thu Jul 18 12:44:03 2024 ———
opened ChimeraX session
> toolshed show
> open
> /Users/justinlee/Downloads/ChimeraX_ISOLDE-1.7.1-cp311-cp311-macosx_10_13_universal2.whl
Unrecognized file suffix '.whl'
> toolshed show
Downloading bundle
ChimeraX_ISOLDE-1.7.1-cp311-cp311-macosx_10_13_universal2.whl
[Repeated 1 time(s)]
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> color #7 #ebebebff
> color #7 #d6d6d6ff
> hide #!7 models
> show #!7 models
> show #!6 models
> hide #!7 models
> color #8 #d6d6d6ff
> color #9 #d6d6d6ff
> color #10 #d6d6d6ff
> color #11 #d6d6d6ff
> color #12 #d6d6d6ff
> hide #!6 models
> show #!6 models
> show #!8 models
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 4/B
> select add #8
4270 atoms, 4390 bonds, 547 residues, 1 model selected
Alignment identifier is 8/A
> select #8/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1-135
1050 atoms, 1076 bonds, 135 residues, 1 model selected
> color sel teal
> select #8/A:547
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/A:456-547
722 atoms, 736 bonds, 92 residues, 1 model selected
> color sel teal
> hide #!6 models
> hide #!8 models
> show #!6 models
> show #!8 models
> hide #!6 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!10 models
> show #!11 models
> show #!12 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!9 models
> show #!6 models
> hide #!9 models
> ui mousemode right select
> select #6/A:491@CZ
1 atom, 1 residue, 1 model selected
> select #6/A:545@CA
1 atom, 1 residue, 1 model selected
> color #12 #eed7acff
> color #12 #ffe5b9ff
[Repeated 1 time(s)]
> show #!12 models
> color #12 #d6d6d6ff
> hide #!12 models
> hide #!6 models
> show #!6 models
> color #6 #ccccccff
> color #6 #ffcc66ff
> color #6 #ff9933ff
> color #6 #cc9933ff
> color #6 #ff9900ff
> color #6 #ffcc66ff
> color #6 #ffcc33ff
> color #6 #ffcc66ff
> color #6 #cc9900ff
> color #6 #996600ff
> color #6 #ffcc33ff
> color #6 #ffcc66ff
> color #6 #ffcc33ff
> color #6 #ffcc66ff
> color #6 #ffcc00ff
> color #6 #cc9900ff
> color #6 #ffcc66ff
> color #6 #999966ff
> color #6 #666633ff
> color #6 #ffffccff
> color #6 #cccc99ff
> color #6 #999966ff
> color #6 #666633ff
> color #6 #333300ff
> color #6 #99ff99ff
> color #6 #33ff66ff
> color #6 #00ccccff
> color #6 #6633ffff
> color #6 #333333ff
> color #6 white
> color #6 #996666ff
> color #6 #ffccccff
> color #6 #cc9999ff
> color #6 #996666ff
> color #6 #330000ff
> color #6 #663333ff
> color #6 #330000ff
> color #6 #ff9999ff
> color #6 #993333ff
> color #6 #660000ff
> color #6 #ff9999ff
> color #6 #cc6666ff
> color #6 #cc3333ff
> color #6 #993333ff
> color #6 #660000ff
> color #6 #ff9999ff
> color #6 #660000ff
> color #8 #666666ff
> color #8 #330000ff
> color #8 #663333ff
> color #8 #330000ff
> color #8 #663333ff
> show #!8 models
> hide #!6 models
> color #8 #996666ff
> color #8 #cc9999ff
> color #8 #ffccccff
> color #8 #663333ff
> color #8 #660000ff
> color #8 #993333ff
> show #!9 models
> color #9 #666666ff
> color #9 #996666ff
> color #8 #660000ff
> show #!6 models
> hide #!6 models
> color #9 #663333ff
> color #10 #333333ff
> color #10 #cc6666ff
> color #11 #cc9999ff
> color #12 black
> color #12 #ffccccff
> hide #!9 models
> select #8/A:467-547
632 atoms, 644 bonds, 81 residues, 1 model selected
> select #8/A:437-547
894 atoms, 917 bonds, 111 residues, 1 model selected
> select
> #8/A:24-30,33-38,51-60,72-76,105-108,121-132,139-147,150-158,161-170,177-187,190-202,210-225,243-252,268-270,273-286,289-291,354-357,361-363,390-403,415-427,429-431,466-474,484-486,521-535,538-546
1759 atoms, 1784 bonds, 215 residues, 1 model selected
> select #8/A:141
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:141-450
2421 atoms, 2498 bonds, 310 residues, 1 model selected
> color sel silver
> select clear
> hide #!8 models
> show #!8 models
> show #!9 models
> hide #!9 models
> hide #!8 models
> show #!9 models
> show #!8 models
> hide #!9 models
> hide #!8 models
> show #!9 models
> show #!8 models
> hide #!9 models
> hide #!8 models
> show #!8 models
> show #!9 models
> show #!10 models
> hide #!9 models
> hide #!10 models
> hide #!8 models
> show #!8 models
> color #3 #ff00ff55
> color #3 #ff00ffb4
> color #3 #ff00ffb5
> select clear
> color #3 #ff00ff7d
> color #3 #ff00ff3e
> hide #!8 models
> show #!8 models
> show #!9 models
> hide #!8 models
> select add #9
4270 atoms, 4390 bonds, 547 residues, 1 model selected
Alignment identifier is 9/A
> select #9/A:141
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:141-450
2421 atoms, 2498 bonds, 310 residues, 1 model selected
> color sel silver
> show #!10 models
> hide #!9 models
> select add #10
6691 atoms, 6888 bonds, 857 residues, 3 models selected
Alignment identifier is 1
> select #9/A:141 #10/A:141
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #9/A:141-450 #10/A:141-450
4842 atoms, 4996 bonds, 620 residues, 2 models selected
1 [ID: 1] region 2 chains [141-450] RMSD: 2.270
> color sel silver
> show #!11 models
> hide #!10 models
Alignment identifier is 2
> select #9/A:141 #10/A:141
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #9/A:141-450 #10/A:141-450
4842 atoms, 4996 bonds, 620 residues, 2 models selected
2 [ID: 2] region 2 chains [141-450] RMSD: 2.270
> color sel silver
> select add #11
9112 atoms, 9386 bonds, 1167 residues, 5 models selected
Alignment identifier is 3
> select #9/A:141 #10/A:141 #11/A:141
27 atoms, 24 bonds, 3 residues, 3 models selected
> select #9/A:141-450 #10/A:141-450 #11/A:141-450
7263 atoms, 7494 bonds, 930 residues, 3 models selected
3 [ID: 3] region 3 chains [141-450] RMSD: 1.747
> color sel silver
> hide #!11 models
> select add #12
11533 atoms, 11884 bonds, 1477 residues, 7 models selected
> show #!12 models
> select add #11
13382 atoms, 13776 bonds, 1714 residues, 8 models selected
> select add #10
15231 atoms, 15668 bonds, 1951 residues, 8 models selected
> select add #9
17080 atoms, 17560 bonds, 2188 residues, 8 models selected
> select subtract #9
12810 atoms, 13170 bonds, 1641 residues, 7 models selected
> select subtract #10
8540 atoms, 8780 bonds, 1094 residues, 5 models selected
> select subtract #11
4270 atoms, 4390 bonds, 547 residues, 3 models selected
Alignment identifier is 12/A
> select #12/A:467-547
632 atoms, 644 bonds, 81 residues, 1 model selected
> select #12/A:375-547
1390 atoms, 1428 bonds, 173 residues, 1 model selected
> select
> #12/A:24-30,33-38,51-60,72-76,105-108,121-132,139-147,151-158,161-170,177-187,190-202,210-225,243-252,268-270,273-289,354-357,361-363,390-403,415-427,429-431,447-449,453-455,466-474,484-486,521-535,538-546
1814 atoms, 1840 bonds, 220 residues, 1 model selected
> select #12/A:141
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/A:141-450
2421 atoms, 2498 bonds, 310 residues, 1 model selected
> color sel silver
> hide #!12 models
> show #!12 models
> select add #12
4270 atoms, 4390 bonds, 547 residues, 2 models selected
> select subtract #12
1 model selected
> hide #!12 models
> show #!7 models
> show #!8 models
> hide #!7 models
> hide #!8 models
> show #!7 models
> show #!8 models
> hide #!8 models
> hide #!7 models
> show #!6 models
> show #!10 models
> show #!8 models
> show #!7 models
> hide #!7 models
> hide #!10 models
> hide #!8 models
> hide #!6 models
> show #!6 models
Downloading bundle
ChimeraX_ISOLDE-1.7.1-cp311-cp311-macosx_10_13_universal2.whl
> hide #!6 models
> show #!7 models
> show #!9 models
> hide #!7 models
> color #3 magenta
> color #3 #ff00ff56
> color #3 #ff00ff00
> color #3 magenta
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!9 models
> select clear
> ui mousemode right translate
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> show #!10 models
> show #!11 models
> show #!12 models
> hide #!12 models
> hide #!11 models
> show #!12 models
> show #!11 models
> hide #!11 models
> hide #!12 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> show #!8 models
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting soft
> save /Users/justinlee/code/oROS-HT_revision/rank1.png width 4000 height 2892
> supersample 4 transparentBackground true
> show #!9 models
> hide #!8 models
> save /Users/justinlee/code/oROS-HT_revision/AF2reruns/rank2.png width 4000
> height 2892 supersample 4 transparentBackground true
> hide #!9 models
> show #!9 models
> show #!7 models
> show #!8 models
> hide #!9 models
> hide #!8 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> save /Users/justinlee/code/oROS-HT_revision/AF2reruns/rank3.png width 4000
> height 2892 supersample 3 transparentBackground true
> hide #!10 models
> show #!11 models
> show #!10 models
> hide #!10 models
> save /Users/justinlee/code/oROS-HT_revision/AF2reruns/rank4.png width 4000
> height 2892 supersample 3 transparentBackground true
> show #!12 models
> hide #!11 models
> save /Users/justinlee/code/oROS-HT_revision/AF2reruns/rank5.png width 4000
> height 2892 supersample 4 transparentBackground true
> open
> /Users/justinlee/Downloads/20240716_Halo5rerun2_d996e_unrelaxed_alphafold2_ptm_model_1_seed_000.r12.pdb
Chain information for
20240716_Halo5rerun2_d996e_unrelaxed_alphafold2_ptm_model_1_seed_000.r12.pdb
#13
---
Chain | Description
A | No description available
> matchmaker #13 to #3
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 6u2m, chain C (#3) with
20240716_Halo5rerun2_d996e_unrelaxed_alphafold2_ptm_model_1_seed_000.r12.pdb,
chain A (#13), sequence alignment score = 1611.6
RMSD between 281 pruned atom pairs is 0.454 angstroms; (across all 383 pairs:
15.325)
> hide #!12 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!8 models
> hide #!7 models
> hide #!8 models
> show #13#!3 surfaces
> hide #!3,13 surfaces
> select add #13
4270 atoms, 4390 bonds, 547 residues, 1 model selected
> show sel surfaces
> open
> /Users/justinlee/Downloads/Halo5rerun2_20240718_d996e_unrelaxed_alphafold2_ptm_model_1_seed_000.r46.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_alphafold2_ptm_model_1_seed_000.r46.pdb
#14
---
Chain | Description
A | No description available
> matchmaker #14 to #3
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 6u2m, chain C (#3) with
Halo5rerun2_20240718_d996e_unrelaxed_alphafold2_ptm_model_1_seed_000.r46.pdb,
chain A (#14), sequence alignment score = 1623.6
RMSD between 281 pruned atom pairs is 0.465 angstroms; (across all 383 pairs:
15.479)
> hide #!13 models
> select add #14
8540 atoms, 8780 bonds, 1094 residues, 3 models selected
> select subtract #13
4270 atoms, 4390 bonds, 547 residues, 2 models selected
> show sel surfaces
[Repeated 1 time(s)]
> hide sel cartoons
> hide sel surfaces
> show sel cartoons
> color bfactor sel
4270 atoms, 547 residues, 1 surfaces, atom bfactor range 28.1 to 98.8
> show #5 models
> hide #!14 models
> show #5#!3 surfaces
> hide #!3,5 surfaces
> hide #!5 models
> show #!14 models
> save /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/halo5rerun3.cxs
> close session
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb
#1
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r1.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r1.pdb
#2
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r2.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r2.pdb
#3
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r3.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r3.pdb
#4
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r4.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r4.pdb
#5
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r5.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r5.pdb
#6
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r6.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r6.pdb
#7
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r7.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r7.pdb
#8
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r8.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r8.pdb
#9
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r9.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r9.pdb
#10
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r10.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r10.pdb
#11
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r11.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r11.pdb
#12
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r12.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r12.pdb
#13
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r13.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r13.pdb
#14
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r14.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r14.pdb
#15
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r15.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r15.pdb
#16
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r16.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r16.pdb
#17
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r17.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r17.pdb
#18
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r18.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r18.pdb
#19
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r19.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r19.pdb
#20
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r20.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r20.pdb
#21
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r21.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r21.pdb
#22
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r22.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r22.pdb
#23
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r23.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r23.pdb
#24
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r24.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r24.pdb
#25
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r25.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r25.pdb
#26
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r26.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r26.pdb
#27
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r27.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r27.pdb
#28
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r28.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r28.pdb
#29
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r29.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r29.pdb
#30
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r30.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r30.pdb
#31
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r31.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r31.pdb
#32
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r32.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r32.pdb
#33
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r33.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r33.pdb
#34
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r34.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r34.pdb
#35
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r35.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r35.pdb
#36
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r36.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r36.pdb
#37
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r37.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r37.pdb
#38
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r38.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r38.pdb
#39
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r39.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r39.pdb
#40
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r40.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r40.pdb
#41
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r41.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r41.pdb
#42
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r42.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r42.pdb
#43
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r43.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r43.pdb
#44
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r44.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r44.pdb
#45
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r45.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r45.pdb
#46
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r46.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r46.pdb
#47
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r47.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r47.pdb
#48
---
Chain | Description
A | No description available
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/20240719_Halo5rerun2/Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r48.pdb
Chain information for
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r48.pdb
#49
---
Chain | Description
A | No description available
> matchmaker #2-48 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
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r1.pdb,
chain A (#2), sequence alignment score = 2819.1
RMSD between 187 pruned atom pairs is 0.280 angstroms; (across all 547 pairs:
11.337)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r2.pdb,
chain A (#3), sequence alignment score = 2814.3
RMSD between 143 pruned atom pairs is 0.277 angstroms; (across all 547 pairs:
12.806)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r3.pdb,
chain A (#4), sequence alignment score = 2805.3
RMSD between 190 pruned atom pairs is 0.332 angstroms; (across all 547 pairs:
12.207)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r4.pdb,
chain A (#5), sequence alignment score = 2814.3
RMSD between 189 pruned atom pairs is 0.356 angstroms; (across all 547 pairs:
12.055)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r5.pdb,
chain A (#6), sequence alignment score = 2814.3
RMSD between 149 pruned atom pairs is 0.375 angstroms; (across all 547 pairs:
12.172)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r6.pdb,
chain A (#7), sequence alignment score = 2826.3
RMSD between 120 pruned atom pairs is 0.839 angstroms; (across all 547 pairs:
9.281)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r7.pdb,
chain A (#8), sequence alignment score = 2826.3
RMSD between 140 pruned atom pairs is 0.845 angstroms; (across all 547 pairs:
9.237)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r8.pdb,
chain A (#9), sequence alignment score = 2826.3
RMSD between 157 pruned atom pairs is 0.864 angstroms; (across all 547 pairs:
9.026)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r9.pdb,
chain A (#10), sequence alignment score = 2829.3
RMSD between 146 pruned atom pairs is 0.863 angstroms; (across all 547 pairs:
8.922)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r10.pdb,
chain A (#11), sequence alignment score = 2829.3
RMSD between 147 pruned atom pairs is 0.869 angstroms; (across all 547 pairs:
9.055)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r11.pdb,
chain A (#12), sequence alignment score = 2832.9
RMSD between 150 pruned atom pairs is 0.868 angstroms; (across all 547 pairs:
9.044)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r12.pdb,
chain A (#13), sequence alignment score = 2823.9
RMSD between 159 pruned atom pairs is 0.898 angstroms; (across all 547 pairs:
8.922)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r13.pdb,
chain A (#14), sequence alignment score = 2829.9
RMSD between 152 pruned atom pairs is 0.877 angstroms; (across all 547 pairs:
8.747)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r14.pdb,
chain A (#15), sequence alignment score = 2826.3
RMSD between 147 pruned atom pairs is 0.881 angstroms; (across all 547 pairs:
8.815)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r15.pdb,
chain A (#16), sequence alignment score = 2829.9
RMSD between 141 pruned atom pairs is 0.877 angstroms; (across all 547 pairs:
8.789)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r16.pdb,
chain A (#17), sequence alignment score = 2836.5
RMSD between 141 pruned atom pairs is 0.891 angstroms; (across all 547 pairs:
8.682)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r17.pdb,
chain A (#18), sequence alignment score = 2829.3
RMSD between 158 pruned atom pairs is 0.895 angstroms; (across all 547 pairs:
8.654)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r18.pdb,
chain A (#19), sequence alignment score = 2832.9
RMSD between 141 pruned atom pairs is 0.895 angstroms; (across all 547 pairs:
8.669)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r19.pdb,
chain A (#20), sequence alignment score = 2836.5
RMSD between 145 pruned atom pairs is 0.900 angstroms; (across all 547 pairs:
8.854)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r20.pdb,
chain A (#21), sequence alignment score = 2832.9
RMSD between 137 pruned atom pairs is 0.918 angstroms; (across all 547 pairs:
8.855)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r21.pdb,
chain A (#22), sequence alignment score = 2832.9
RMSD between 147 pruned atom pairs is 0.913 angstroms; (across all 547 pairs:
8.596)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r22.pdb,
chain A (#23), sequence alignment score = 2820.3
RMSD between 152 pruned atom pairs is 0.903 angstroms; (across all 547 pairs:
8.756)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r23.pdb,
chain A (#24), sequence alignment score = 2820.9
RMSD between 140 pruned atom pairs is 0.908 angstroms; (across all 547 pairs:
8.821)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r24.pdb,
chain A (#25), sequence alignment score = 2826.3
RMSD between 137 pruned atom pairs is 0.900 angstroms; (across all 547 pairs:
8.834)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r25.pdb,
chain A (#26), sequence alignment score = 2826.3
RMSD between 145 pruned atom pairs is 0.905 angstroms; (across all 547 pairs:
8.729)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r26.pdb,
chain A (#27), sequence alignment score = 2823.9
RMSD between 144 pruned atom pairs is 0.913 angstroms; (across all 547 pairs:
8.871)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r27.pdb,
chain A (#28), sequence alignment score = 2826.3
RMSD between 149 pruned atom pairs is 0.904 angstroms; (across all 547 pairs:
8.885)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r28.pdb,
chain A (#29), sequence alignment score = 2826.3
RMSD between 140 pruned atom pairs is 0.900 angstroms; (across all 547 pairs:
8.725)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r29.pdb,
chain A (#30), sequence alignment score = 2822.7
RMSD between 154 pruned atom pairs is 0.913 angstroms; (across all 547 pairs:
8.692)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r30.pdb,
chain A (#31), sequence alignment score = 2825.7
RMSD between 139 pruned atom pairs is 0.909 angstroms; (across all 547 pairs:
8.680)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r31.pdb,
chain A (#32), sequence alignment score = 2829.3
RMSD between 141 pruned atom pairs is 0.886 angstroms; (across all 547 pairs:
8.681)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r32.pdb,
chain A (#33), sequence alignment score = 2822.7
RMSD between 141 pruned atom pairs is 0.908 angstroms; (across all 547 pairs:
8.689)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r33.pdb,
chain A (#34), sequence alignment score = 2819.7
RMSD between 134 pruned atom pairs is 0.882 angstroms; (across all 547 pairs:
8.721)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r34.pdb,
chain A (#35), sequence alignment score = 2832.9
RMSD between 138 pruned atom pairs is 0.889 angstroms; (across all 547 pairs:
8.698)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r35.pdb,
chain A (#36), sequence alignment score = 2830.5
RMSD between 125 pruned atom pairs is 0.895 angstroms; (across all 547 pairs:
8.849)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r36.pdb,
chain A (#37), sequence alignment score = 2823.9
RMSD between 121 pruned atom pairs is 0.903 angstroms; (across all 547 pairs:
8.808)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r37.pdb,
chain A (#38), sequence alignment score = 2823.9
RMSD between 142 pruned atom pairs is 0.903 angstroms; (across all 547 pairs:
8.656)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r38.pdb,
chain A (#39), sequence alignment score = 2836.5
RMSD between 154 pruned atom pairs is 0.915 angstroms; (across all 547 pairs:
8.734)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r39.pdb,
chain A (#40), sequence alignment score = 2832.9
RMSD between 154 pruned atom pairs is 0.928 angstroms; (across all 547 pairs:
8.625)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r40.pdb,
chain A (#41), sequence alignment score = 2826.3
RMSD between 135 pruned atom pairs is 0.916 angstroms; (across all 547 pairs:
8.678)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r41.pdb,
chain A (#42), sequence alignment score = 2811.9
RMSD between 154 pruned atom pairs is 0.907 angstroms; (across all 547 pairs:
8.521)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r42.pdb,
chain A (#43), sequence alignment score = 2826.3
RMSD between 137 pruned atom pairs is 0.905 angstroms; (across all 547 pairs:
8.626)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r43.pdb,
chain A (#44), sequence alignment score = 2826.3
RMSD between 132 pruned atom pairs is 0.898 angstroms; (across all 547 pairs:
8.753)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r44.pdb,
chain A (#45), sequence alignment score = 2822.7
RMSD between 131 pruned atom pairs is 0.915 angstroms; (across all 547 pairs:
8.854)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r45.pdb,
chain A (#46), sequence alignment score = 2815.5
RMSD between 145 pruned atom pairs is 0.918 angstroms; (across all 547 pairs:
8.734)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r46.pdb,
chain A (#47), sequence alignment score = 2829.9
RMSD between 155 pruned atom pairs is 0.919 angstroms; (across all 547 pairs:
8.737)
Matchmaker
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r0.pdb,
chain A (#1) with
Halo5rerun2_20240718_d996e_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.r47.pdb,
chain A (#48), sequence alignment score = 2829.3
RMSD between 139 pruned atom pairs is 0.925 angstroms; (across all 547 pairs:
8.877)
> save /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/model3_halo5rerun2.pdb
> close session
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/model3_halo5rerun2.pdb
Chain information for model3_halo5rerun2.pdb
---
Chain | Description
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A 1.22/A 1.23/A
1.24/A 1.25/A 1.26/A 1.27/A 1.28/A 1.29/A 1.30/A 1.31/A 1.32/A 1.33/A 1.34/A
1.35/A 1.36/A 1.37/A 1.38/A 1.39/A 1.40/A 1.41/A 1.42/A 1.43/A 1.44/A 1.45/A
1.46/A 1.47/A 1.48/A 1.49/A | No description available
> ui tool show "Molecular Dynamics Viewer"
Please register the custom scheme 'kmd' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.
> close
Chain information for structure #1
---
Chain | Description
A | No description available
> close
> open /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/model3_halo5rerun2.pdb format pdb
Chain information for model3_halo5rerun2.pdb
---
Chain | Description
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A 1.22/A 1.23/A
1.24/A 1.25/A 1.26/A 1.27/A 1.28/A 1.29/A 1.30/A 1.31/A 1.32/A 1.33/A 1.34/A
1.35/A 1.36/A 1.37/A 1.38/A 1.39/A 1.40/A 1.41/A 1.42/A 1.43/A 1.44/A 1.45/A
1.46/A 1.47/A 1.48/A 1.49/A | No description available
> open 6u2m
6u2m title:
Crystal structure of a HaloTag-based calcium indicator, HaloCaMP V2, bound to
JF635 [more info...]
Chain information for 6u2m #2
---
Chain | Description
A C | HaloCaMP V2
Non-standard residues in 6u2m #2
---
CA — calcium ion
CL — chloride ion
PUJ —
(1E,3S)-1-{10-[2-carboxy-5-({2-[2-(hexyloxy)ethoxy]ethyl}carbamoyl)phenyl]-7-(3-fluoroazetidin-1-yl)-5,5-dimethyldibenz
o[b,e]silin-3(5H)-ylidene}-3-fluoroazetidin-1-ium (JF635)
6u2m mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> matchmaker #1 to #2
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 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.1),
sequence alignment score = 1594.2
RMSD between 280 pruned atom pairs is 0.512 angstroms; (across all 383 pairs:
13.813)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.2),
sequence alignment score = 1612.1
RMSD between 281 pruned atom pairs is 0.394 angstroms; (across all 383 pairs:
14.613)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.3),
sequence alignment score = 1617.6
RMSD between 281 pruned atom pairs is 0.394 angstroms; (across all 383 pairs:
14.930)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.4),
sequence alignment score = 1614.5
RMSD between 281 pruned atom pairs is 0.400 angstroms; (across all 383 pairs:
15.101)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.5),
sequence alignment score = 1617.6
RMSD between 281 pruned atom pairs is 0.410 angstroms; (across all 383 pairs:
15.146)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.6),
sequence alignment score = 1617.6
RMSD between 281 pruned atom pairs is 0.411 angstroms; (across all 383 pairs:
15.136)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.7),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.416 angstroms; (across all 383 pairs:
15.144)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.8),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.420 angstroms; (across all 383 pairs:
15.155)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.9),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.419 angstroms; (across all 383 pairs:
15.128)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.10),
sequence alignment score = 1626
RMSD between 281 pruned atom pairs is 0.423 angstroms; (across all 383 pairs:
15.138)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.11),
sequence alignment score = 1626
RMSD between 281 pruned atom pairs is 0.428 angstroms; (across all 383 pairs:
15.149)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.12),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.432 angstroms; (across all 383 pairs:
15.159)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.13),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.438 angstroms; (across all 383 pairs:
15.173)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.14),
sequence alignment score = 1626.6
RMSD between 281 pruned atom pairs is 0.443 angstroms; (across all 383 pairs:
15.116)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.15),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.447 angstroms; (across all 383 pairs:
15.121)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.16),
sequence alignment score = 1626.6
RMSD between 281 pruned atom pairs is 0.444 angstroms; (across all 383 pairs:
15.112)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.17),
sequence alignment score = 1623.6
RMSD between 281 pruned atom pairs is 0.445 angstroms; (across all 383 pairs:
15.128)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.18),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.448 angstroms; (across all 383 pairs:
15.106)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.19),
sequence alignment score = 1626.6
RMSD between 281 pruned atom pairs is 0.446 angstroms; (across all 383 pairs:
15.045)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.20),
sequence alignment score = 1623.6
RMSD between 281 pruned atom pairs is 0.443 angstroms; (across all 383 pairs:
15.138)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.21),
sequence alignment score = 1626.6
RMSD between 281 pruned atom pairs is 0.445 angstroms; (across all 383 pairs:
15.152)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.22),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.445 angstroms; (across all 383 pairs:
15.063)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.23),
sequence alignment score = 1632.6
RMSD between 281 pruned atom pairs is 0.450 angstroms; (across all 383 pairs:
15.086)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.24),
sequence alignment score = 1614.6
RMSD between 281 pruned atom pairs is 0.446 angstroms; (across all 383 pairs:
15.045)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.25),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.448 angstroms; (across all 383 pairs:
15.125)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.26),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.457 angstroms; (across all 383 pairs:
15.122)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.27),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.453 angstroms; (across all 383 pairs:
15.155)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.28),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.453 angstroms; (across all 383 pairs:
15.131)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.29),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.453 angstroms; (across all 383 pairs:
15.121)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.30),
sequence alignment score = 1632.6
RMSD between 281 pruned atom pairs is 0.456 angstroms; (across all 383 pairs:
15.142)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.31),
sequence alignment score = 1632.6
RMSD between 281 pruned atom pairs is 0.459 angstroms; (across all 383 pairs:
15.131)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.32),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.454 angstroms; (across all 383 pairs:
15.120)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.33),
sequence alignment score = 1632.6
RMSD between 281 pruned atom pairs is 0.456 angstroms; (across all 383 pairs:
15.106)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.34),
sequence alignment score = 1635.6
RMSD between 281 pruned atom pairs is 0.460 angstroms; (across all 383 pairs:
15.149)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.35),
sequence alignment score = 1626.6
RMSD between 281 pruned atom pairs is 0.454 angstroms; (across all 383 pairs:
15.082)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.36),
sequence alignment score = 1626.6
RMSD between 281 pruned atom pairs is 0.454 angstroms; (across all 383 pairs:
15.097)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.37),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.453 angstroms; (across all 383 pairs:
15.150)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.38),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.455 angstroms; (across all 383 pairs:
15.085)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.39),
sequence alignment score = 1623.6
RMSD between 281 pruned atom pairs is 0.455 angstroms; (across all 383 pairs:
15.095)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.40),
sequence alignment score = 1626.6
RMSD between 281 pruned atom pairs is 0.448 angstroms; (across all 383 pairs:
15.075)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.41),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.452 angstroms; (across all 383 pairs:
15.112)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.42),
sequence alignment score = 1628.4
RMSD between 281 pruned atom pairs is 0.456 angstroms; (across all 383 pairs:
15.098)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.43),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.457 angstroms; (across all 383 pairs:
15.045)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.44),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.453 angstroms; (across all 383 pairs:
15.029)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.45),
sequence alignment score = 1632.6
RMSD between 281 pruned atom pairs is 0.455 angstroms; (across all 383 pairs:
15.121)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.46),
sequence alignment score = 1625.4
RMSD between 281 pruned atom pairs is 0.457 angstroms; (across all 383 pairs:
15.062)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.47),
sequence alignment score = 1626.6
RMSD between 281 pruned atom pairs is 0.453 angstroms; (across all 383 pairs:
15.079)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.48),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.454 angstroms; (across all 383 pairs:
15.100)
Matchmaker 6u2m, chain C (#2) with model3_halo5rerun2.pdb, chain A (#1.49),
sequence alignment score = 1629.6
RMSD between 281 pruned atom pairs is 0.454 angstroms; (across all 383 pairs:
15.085)
> close #2
> save /Users/justinlee/code/oROS-
> HT_revision/Prediction/Halo5_AF2reruns/model3_halo5rerun2.pdb
> close
Chain information for structure #1
---
Chain | Description
A | No description available
> close
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
[deleted a bunch of these to fit within ticket size limits]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 375, in thread_safe
func(*args, **kw)
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 60, in handle_scheme
self.changeModel(frame, command[12] == 'T')
File "/Users/justinlee/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 140, in changeModel
atms = self.atomStruct.atoms
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 174, in get_prop
vcount = getattr(self, value_count)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 106, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,2
Model Number: MMQW3LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3.1 (23D60)
Kernel Version: Darwin 23.3.0
Time since boot: 68 days, 11 hours, 34 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
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
LG HDR 4K:
Resolution: 6016 x 3384
UI Looks like: 3008 x 1692 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
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: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
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: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
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: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
MolecularDynamicsViewer: 1.4
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
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: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (6)
comment:1 by , 15 months ago
| Component: | Unassigned → Third Party |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MD Viewer: 'close' during playback produce traceback |
comment:3 by , 15 months ago
Hi Kyle,
It seems that your editor address for the bundle is "kdiller99.junk@…".
--Eric
comment:4 by , 15 months ago
Once you are logged in as an editor, you could add additional email addresses as editors to lessen the chance of this happening in the future...
comment:5 by , 15 months ago
Thanks for finding the email. Uploaded version 1.5 that fixes this issue. On Mon, Jul 29, 2024 at 2:20 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: > >
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