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Opened 6 months ago
Closed 6 months ago
#17672 closed defect (duplicate)
Safesave: file missing
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.12.28-1-lts-x86_64-with-glibc2.38
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /home/lukah/Downloads/output/_167_9/_167_9.pdb_unrelaxed_rank_005_alphafold2_ptm_model_3_seed_000.pdb
Chain information for
_167_9.pdb_unrelaxed_rank_005_alphafold2_ptm_model_3_seed_000.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> open
> /home/lukah/Downloads/TEVp-250512-ppi28-combined/filtered_sequences/filtered_binders/_167_9.pdb
Chain information for _167_9.pdb #2
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 _167_9.pdb_unrelaxed_rank_005_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with _167_9.pdb, chain A (#2), sequence alignment score = 1066
RMSD between 192 pruned atom pairs is 0.647 angstroms; (across all 214 pairs:
2.313)
> matchmaker #2 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 _167_9.pdb_unrelaxed_rank_005_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with _167_9.pdb, chain A (#2), sequence alignment score = 1066
RMSD between 192 pruned atom pairs is 0.647 angstroms; (across all 214 pairs:
2.313)
> open
> /home/lukah/Downloads/output/_167_9/_167_9.pdb_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
Chain information for
_167_9.pdb_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #3
---
Chain | Description
A | No description available
> open
> /home/lukah/Downloads/output/_167_9/_167_9.pdb_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb
Chain information for
_167_9.pdb_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb #4
---
Chain | Description
A | No description available
> open
> /home/lukah/Downloads/output/_167_9/_167_9.pdb_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000.pdb
Chain information for
_167_9.pdb_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000.pdb #5
---
Chain | Description
A | No description available
> open
> /home/lukah/Downloads/output/_167_9/_167_9.pdb_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb
Chain information for
_167_9.pdb_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb #6
---
Chain | Description
A | No description available
Computing secondary structure
[Repeated 3 time(s)]
> ui tool show Matchmaker
> matchmaker #2-6 to #1
Computing secondary structure
[Repeated 5 time(s)] 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 _167_9.pdb_unrelaxed_rank_005_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with _167_9.pdb, chain A (#2), sequence alignment score = 1066
RMSD between 192 pruned atom pairs is 0.647 angstroms; (across all 214 pairs:
2.313)
Matchmaker _167_9.pdb_unrelaxed_rank_005_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
_167_9.pdb_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb, chain A
(#3), sequence alignment score = 1444.5
RMSD between 197 pruned atom pairs is 0.398 angstroms; (across all 281 pairs:
11.326)
Matchmaker _167_9.pdb_unrelaxed_rank_005_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
_167_9.pdb_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#4), sequence alignment score = 1444.5
RMSD between 195 pruned atom pairs is 0.438 angstroms; (across all 281 pairs:
12.456)
Matchmaker _167_9.pdb_unrelaxed_rank_005_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
_167_9.pdb_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#5), sequence alignment score = 1450.5
RMSD between 203 pruned atom pairs is 0.437 angstroms; (across all 281 pairs:
9.988)
Matchmaker _167_9.pdb_unrelaxed_rank_005_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
_167_9.pdb_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#6), sequence alignment score = 1441.5
RMSD between 203 pruned atom pairs is 0.439 angstroms; (across all 281 pairs:
10.858)
> matchmaker #2-6 to #1
Computing secondary structure
[Repeated 5 time(s)] 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 _167_9.pdb_unrelaxed_rank_005_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with _167_9.pdb, chain A (#2), sequence alignment score = 1066
RMSD between 192 pruned atom pairs is 0.647 angstroms; (across all 214 pairs:
2.313)
Matchmaker _167_9.pdb_unrelaxed_rank_005_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
_167_9.pdb_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb, chain A
(#3), sequence alignment score = 1444.5
RMSD between 197 pruned atom pairs is 0.398 angstroms; (across all 281 pairs:
11.326)
Matchmaker _167_9.pdb_unrelaxed_rank_005_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
_167_9.pdb_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#4), sequence alignment score = 1444.5
RMSD between 195 pruned atom pairs is 0.438 angstroms; (across all 281 pairs:
12.456)
Matchmaker _167_9.pdb_unrelaxed_rank_005_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
_167_9.pdb_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#5), sequence alignment score = 1450.5
RMSD between 203 pruned atom pairs is 0.437 angstroms; (across all 281 pairs:
9.988)
Matchmaker _167_9.pdb_unrelaxed_rank_005_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
_167_9.pdb_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#6), sequence alignment score = 1441.5
RMSD between 203 pruned atom pairs is 0.439 angstroms; (across all 281 pairs:
10.858)
> close session
> open
> /home/lukah/Downloads/output/_269_24/_269_24.pdb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
Chain information for
_269_24.pdb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> open
> /home/lukah/Downloads/output/_269_24/_269_24.pdb_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb
Chain information for
_269_24.pdb_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb #2
---
Chain | Description
A | No description available
> open
> /home/lukah/Downloads/output/_269_24/_269_24.pdb_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb
Chain information for
_269_24.pdb_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb #3
---
Chain | Description
A | No description available
> open
> /home/lukah/Downloads/output/_269_24/_269_24.pdb_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb
Chain information for
_269_24.pdb_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb #4
---
Chain | Description
A | No description available
> open
> /home/lukah/Downloads/output/_269_24/_269_24.pdb_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb
Chain information for
_269_24.pdb_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb #5
---
Chain | Description
A | No description available
Computing secondary structure
[Repeated 3 time(s)]
> open
> /home/lukah/Downloads/TEVp-250512-ppi28-combined/filtered_sequences/filtered_binders/_269_24.pdb
Chain information for _269_24.pdb #6
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2-6 to #1
Computing secondary structure
[Repeated 5 time(s)] 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 _269_24.pdb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
_269_24.pdb_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#2), sequence alignment score = 1445.1
RMSD between 205 pruned atom pairs is 0.437 angstroms; (across all 281 pairs:
6.059)
Matchmaker _269_24.pdb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
_269_24.pdb_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb, chain A
(#3), sequence alignment score = 1433.1
RMSD between 211 pruned atom pairs is 0.437 angstroms; (across all 281 pairs:
8.908)
Matchmaker _269_24.pdb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
_269_24.pdb_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#4), sequence alignment score = 1440.3
RMSD between 211 pruned atom pairs is 0.489 angstroms; (across all 281 pairs:
6.815)
Matchmaker _269_24.pdb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
_269_24.pdb_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#5), sequence alignment score = 1414.5
RMSD between 211 pruned atom pairs is 0.441 angstroms; (across all 281 pairs:
6.596)
Matchmaker _269_24.pdb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with _269_24.pdb, chain A (#6), sequence alignment score = 1056.1
RMSD between 196 pruned atom pairs is 0.580 angstroms; (across all 214 pairs:
1.405)
> matchmaker #2-6 to #1
Computing secondary structure
[Repeated 5 time(s)] 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 _269_24.pdb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
_269_24.pdb_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#2), sequence alignment score = 1445.1
RMSD between 205 pruned atom pairs is 0.437 angstroms; (across all 281 pairs:
6.059)
Matchmaker _269_24.pdb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
_269_24.pdb_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb, chain A
(#3), sequence alignment score = 1433.1
RMSD between 211 pruned atom pairs is 0.437 angstroms; (across all 281 pairs:
8.908)
Matchmaker _269_24.pdb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
_269_24.pdb_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#4), sequence alignment score = 1440.3
RMSD between 211 pruned atom pairs is 0.489 angstroms; (across all 281 pairs:
6.815)
Matchmaker _269_24.pdb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
_269_24.pdb_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#5), sequence alignment score = 1414.5
RMSD between 211 pruned atom pairs is 0.441 angstroms; (across all 281 pairs:
6.596)
Matchmaker _269_24.pdb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with _269_24.pdb, chain A (#6), sequence alignment score = 1056.1
RMSD between 196 pruned atom pairs is 0.580 angstroms; (across all 214 pairs:
1.405)
> close session
> open
> /home/lukah/Downloads/output/TEVp-250503-anchor-235-3_0_285_6/TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
Chain information for
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#1
---
Chain | Description
A | No description available
Computing secondary structure
> open
> /home/lukah/Downloads/output/TEVp-250503-anchor-235-3_0_285_6/TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000.pdb
Chain information for
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000.pdb
#2
---
Chain | Description
A | No description available
> open
> /home/lukah/Downloads/output/TEVp-250503-anchor-235-3_0_285_6/TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb
Chain information for
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb
#3
---
Chain | Description
A | No description available
> open
> /home/lukah/Downloads/output/TEVp-250503-anchor-235-3_0_285_6/TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb
Chain information for
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb
#4
---
Chain | Description
A | No description available
> open
> /home/lukah/Downloads/output/TEVp-250503-anchor-235-3_0_285_6/TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb
Chain information for
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb
#5
---
Chain | Description
A | No description available
Computing secondary structure
[Repeated 3 time(s)]
> open /home/lukah/Faks/2-stopnja/magistrsko-
> delo/design/output/TEVp-250512-anchor-
> combined/filtered_sequences/filtered_binders/TEVp-250503-anchor-235-3_0_285_6.pdb
Chain information for TEVp-250503-anchor-235-3_0_285_6.pdb #6
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2-6 to #1
Computing secondary structure
[Repeated 5 time(s)] 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
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000.pdb,
chain A (#2), sequence alignment score = 1597.5
RMSD between 297 pruned atom pairs is 0.483 angstroms; (across all 305 pairs:
0.705)
Matchmaker
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#3), sequence alignment score = 1560.9
RMSD between 204 pruned atom pairs is 0.522 angstroms; (across all 305 pairs:
9.324)
Matchmaker
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb,
chain A (#4), sequence alignment score = 1558.2
RMSD between 200 pruned atom pairs is 0.395 angstroms; (across all 305 pairs:
12.022)
Matchmaker
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#5), sequence alignment score = 1554.3
RMSD between 205 pruned atom pairs is 0.513 angstroms; (across all 305 pairs:
12.047)
Matchmaker
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with TEVp-250503-anchor-235-3_0_285_6.pdb, chain A (#6), sequence
alignment score = 1147.5
RMSD between 214 pruned atom pairs is 0.448 angstroms; (across all 222 pairs:
1.136)
> matchmaker #2-6 to #1
Computing secondary structure
[Repeated 5 time(s)] 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
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000.pdb,
chain A (#2), sequence alignment score = 1597.5
RMSD between 297 pruned atom pairs is 0.483 angstroms; (across all 305 pairs:
0.705)
Matchmaker
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#3), sequence alignment score = 1560.9
RMSD between 204 pruned atom pairs is 0.522 angstroms; (across all 305 pairs:
9.324)
Matchmaker
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb,
chain A (#4), sequence alignment score = 1558.2
RMSD between 200 pruned atom pairs is 0.395 angstroms; (across all 305 pairs:
12.022)
Matchmaker
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#5), sequence alignment score = 1554.3
RMSD between 205 pruned atom pairs is 0.513 angstroms; (across all 305 pairs:
12.047)
Matchmaker
TEVp-250503-anchor-235-3_0_285_6.pdb_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with TEVp-250503-anchor-235-3_0_285_6.pdb, chain A (#6), sequence
alignment score = 1147.5
RMSD between 214 pruned atom pairs is 0.448 angstroms; (across all 222 pairs:
1.136)
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> close session
> open
> /home/lukah/Downloads/output/TEVp_motifbinder_ppi_A28_8_5_11/TEVp_motifbinder_ppi_A28_8_5_11.pdb_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
Chain information for
TEVp_motifbinder_ppi_A28_8_5_11.pdb_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
#1
---
Chain | Description
A | No description available
Computing secondary structure
> open /home/lukah/Downloads/TEVp-250512-anchor-
> fin/pdbs/TEVp_motifbinder_ppi_A28_8_5_11.pdb
Chain information for TEVp_motifbinder_ppi_A28_8_5_11.pdb #2
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2 to #1
Computing secondary structure
[Repeated 1 time(s)] 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
TEVp_motifbinder_ppi_A28_8_5_11.pdb_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#1) with TEVp_motifbinder_ppi_A28_8_5_11.pdb, chain A (#2), sequence
alignment score = 1133.4
RMSD between 209 pruned atom pairs is 0.572 angstroms; (across all 219 pairs:
0.998)
> matchmaker #2 to #1
Computing secondary structure
[Repeated 1 time(s)] 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
TEVp_motifbinder_ppi_A28_8_5_11.pdb_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#1) with TEVp_motifbinder_ppi_A28_8_5_11.pdb, chain A (#2), sequence
alignment score = 1133.4
RMSD between 209 pruned atom pairs is 0.572 angstroms; (across all 219 pairs:
0.998)
> close session
> open /home/lukah/Downloads/TEVp-250512-anchor-
> fin/pdbs/TEVp_motifbinder_ppi_A28_32_3_1.pdb
Chain information for TEVp_motifbinder_ppi_A28_32_3_1.pdb #1
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> open
> /home/lukah/Downloads/output/TEVp_motifbinder_ppi_A28_32_3_1/TEVp_motifbinder_ppi_A28_32_3_1.pdb_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
Chain information for
TEVp_motifbinder_ppi_A28_32_3_1.pdb_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
#2
---
Chain | Description
A | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 TEVp_motifbinder_ppi_A28_32_3_1.pdb, chain A (#1) with
TEVp_motifbinder_ppi_A28_32_3_1.pdb_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb,
chain A (#2), sequence alignment score = 1131
RMSD between 207 pruned atom pairs is 0.564 angstroms; (across all 219 pairs:
0.929)
> matchmaker #2 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 TEVp_motifbinder_ppi_A28_32_3_1.pdb, chain A (#1) with
TEVp_motifbinder_ppi_A28_32_3_1.pdb_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb,
chain A (#2), sequence alignment score = 1131
RMSD between 207 pruned atom pairs is 0.564 angstroms; (across all 219 pairs:
0.929)
> hide #2 models
> show #2 models
Traceback (most recent call last):
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 109,
in __exit__
os.replace(self._tmp_filename, self.name)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp' ->
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/lib/python3.11/site-packages/chimerax/ui/gui.py", line 998, in
resizeEvent
self.session.ui.settings.last_window_size = wh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/lib/python3.11/site-packages/chimerax/core/settings.py", line 199,
in __setattr__
ConfigFile.__setattr__(self, name, value)
File "/app/lib/python3.11/site-packages/chimerax/core/configfile.py", line
386, in __setattr__
ConfigFile.save(self)
File "/app/lib/python3.11/site-packages/chimerax/core/configfile.py", line
335, in save
with SaveTextFile(self._filename) as f:
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 128,
in __exit__
os.remove(self._tmp_filename)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp'
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp'
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 128,
in __exit__
os.remove(self._tmp_filename)
See log for complete Python traceback.
Traceback (most recent call last):
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 109,
in __exit__
os.replace(self._tmp_filename, self.name)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp' ->
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/lib/python3.11/site-packages/chimerax/ui/gui.py", line 998, in
resizeEvent
self.session.ui.settings.last_window_size = wh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/lib/python3.11/site-packages/chimerax/core/settings.py", line 199,
in __setattr__
ConfigFile.__setattr__(self, name, value)
File "/app/lib/python3.11/site-packages/chimerax/core/configfile.py", line
386, in __setattr__
ConfigFile.save(self)
File "/app/lib/python3.11/site-packages/chimerax/core/configfile.py", line
335, in save
with SaveTextFile(self._filename) as f:
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 128,
in __exit__
os.remove(self._tmp_filename)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp'
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp'
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 128,
in __exit__
os.remove(self._tmp_filename)
See log for complete Python traceback.
Traceback (most recent call last):
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 109,
in __exit__
os.replace(self._tmp_filename, self.name)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp' ->
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/lib/python3.11/site-packages/chimerax/ui/gui.py", line 998, in
resizeEvent
self.session.ui.settings.last_window_size = wh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/lib/python3.11/site-packages/chimerax/core/settings.py", line 199,
in __setattr__
ConfigFile.__setattr__(self, name, value)
File "/app/lib/python3.11/site-packages/chimerax/core/configfile.py", line
386, in __setattr__
ConfigFile.save(self)
File "/app/lib/python3.11/site-packages/chimerax/core/configfile.py", line
335, in save
with SaveTextFile(self._filename) as f:
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 128,
in __exit__
os.remove(self._tmp_filename)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp'
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp'
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 128,
in __exit__
os.remove(self._tmp_filename)
See log for complete Python traceback.
Traceback (most recent call last):
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 109,
in __exit__
os.replace(self._tmp_filename, self.name)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp' ->
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/lib/python3.11/site-packages/chimerax/ui/gui.py", line 998, in
resizeEvent
self.session.ui.settings.last_window_size = wh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/lib/python3.11/site-packages/chimerax/core/settings.py", line 199,
in __setattr__
ConfigFile.__setattr__(self, name, value)
File "/app/lib/python3.11/site-packages/chimerax/core/configfile.py", line
386, in __setattr__
ConfigFile.save(self)
File "/app/lib/python3.11/site-packages/chimerax/core/configfile.py", line
335, in save
with SaveTextFile(self._filename) as f:
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 128,
in __exit__
os.remove(self._tmp_filename)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp'
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp'
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 128,
in __exit__
os.remove(self._tmp_filename)
See log for complete Python traceback.
Traceback (most recent call last):
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 109,
in __exit__
os.replace(self._tmp_filename, self.name)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp' ->
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/lib/python3.11/site-packages/chimerax/ui/gui.py", line 998, in
resizeEvent
self.session.ui.settings.last_window_size = wh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/lib/python3.11/site-packages/chimerax/core/settings.py", line 199,
in __setattr__
ConfigFile.__setattr__(self, name, value)
File "/app/lib/python3.11/site-packages/chimerax/core/configfile.py", line
386, in __setattr__
ConfigFile.save(self)
File "/app/lib/python3.11/site-packages/chimerax/core/configfile.py", line
335, in save
with SaveTextFile(self._filename) as f:
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 128,
in __exit__
os.remove(self._tmp_filename)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp'
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp'
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 128,
in __exit__
os.remove(self._tmp_filename)
See log for complete Python traceback.
Traceback (most recent call last):
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 109,
in __exit__
os.replace(self._tmp_filename, self.name)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp' ->
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/lib/python3.11/site-packages/chimerax/ui/gui.py", line 998, in
resizeEvent
self.session.ui.settings.last_window_size = wh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/lib/python3.11/site-packages/chimerax/core/settings.py", line 199,
in __setattr__
ConfigFile.__setattr__(self, name, value)
File "/app/lib/python3.11/site-packages/chimerax/core/configfile.py", line
386, in __setattr__
ConfigFile.save(self)
File "/app/lib/python3.11/site-packages/chimerax/core/configfile.py", line
335, in save
with SaveTextFile(self._filename) as f:
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 128,
in __exit__
os.remove(self._tmp_filename)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp'
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp'
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 128,
in __exit__
os.remove(self._tmp_filename)
See log for complete Python traceback.
Traceback (most recent call last):
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 109,
in __exit__
os.replace(self._tmp_filename, self.name)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp' ->
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/lib/python3.11/site-packages/chimerax/ui/gui.py", line 998, in
resizeEvent
self.session.ui.settings.last_window_size = wh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/lib/python3.11/site-packages/chimerax/core/settings.py", line 199,
in __setattr__
ConfigFile.__setattr__(self, name, value)
File "/app/lib/python3.11/site-packages/chimerax/core/configfile.py", line
386, in __setattr__
ConfigFile.save(self)
File "/app/lib/python3.11/site-packages/chimerax/core/configfile.py", line
335, in save
with SaveTextFile(self._filename) as f:
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 128,
in __exit__
os.remove(self._tmp_filename)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp'
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp'
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 128,
in __exit__
os.remove(self._tmp_filename)
See log for complete Python traceback.
Traceback (most recent call last):
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 109,
in __exit__
os.replace(self._tmp_filename, self.name)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp' ->
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/lib/python3.11/site-packages/chimerax/ui/gui.py", line 998, in
resizeEvent
self.session.ui.settings.last_window_size = wh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/lib/python3.11/site-packages/chimerax/core/settings.py", line 199,
in __setattr__
ConfigFile.__setattr__(self, name, value)
File "/app/lib/python3.11/site-packages/chimerax/core/configfile.py", line
386, in __setattr__
ConfigFile.save(self)
File "/app/lib/python3.11/site-packages/chimerax/core/configfile.py", line
335, in save
with SaveTextFile(self._filename) as f:
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 128,
in __exit__
os.remove(self._tmp_filename)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp'
FileNotFoundError: [Errno 2] No such file or directory:
'/home/lukah/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp'
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 128,
in __exit__
os.remove(self._tmp_filename)
See log for complete Python traceback.
OpenGL version: 4.6 (Core Profile) Mesa 25.0.3 (git-c3afa2a74f)
OpenGL renderer: AMD Radeon RX 6700 XT (radeonsi, navi22, LLVM 17.0.6, DRM 3.61, 6.12.28-1-lts)
OpenGL vendor: AMD
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=plasmax11
XDG_SESSION_DESKTOP=KDE
XDG_CURRENT_DESKTOP=KDE
DISPLAY=:0
Manufacturer: To Be Filled By O.E.M.
Model: B450M-HDV R4.0
OS: Freedesktop SDK 23.08
Architecture: 64bit ELF
Virtual Machine: detection failed
CPU: 16 AMD Ryzen 7 5700X3D 8-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 23Gi 6.6Gi 426Mi 2.2Gi 8.0Gi
Swap: 15Gi 15Gi 14Mi
Graphics:
0a:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Navi 22 [Radeon RX 6700/6700 XT/6750 XT / 6800M/6850M XT] [1002:73df] (rev c5)
Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:3982]
Kernel driver in use: amdgpu
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 6 months ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Safesave: file missing |
comment:2 by , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Duplicate of #16631