AlphaFold JSON opened as MOLE JSON

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold predictions/Top 5 full-
> length PUS7L structures overlayed .cxs"

Log from Thu Mar 16 13:39:25 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7L_af5cb_FullHumanPUS7L
> structure/PUS7L_af5cb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"

Chain information for
PUS7L_af5cb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7L_af5cb_FullHumanPUS7L
> structure/PUS7L_af5cb_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000.pdb"

Chain information for
PUS7L_af5cb_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7L_af5cb_FullHumanPUS7L
> structure/PUS7L_af5cb_unrelaxed_rank_003_alphafold2_ptm_model_4_seed_000.pdb"

Chain information for
PUS7L_af5cb_unrelaxed_rank_003_alphafold2_ptm_model_4_seed_000.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7L_af5cb_FullHumanPUS7L
> structure/PUS7L_af5cb_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb"

Chain information for
PUS7L_af5cb_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7L_af5cb_FullHumanPUS7L
> structure/PUS7L_af5cb_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb"

Chain information for
PUS7L_af5cb_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb #5  
---  
Chain | Description  
A | No description available  
  

> hide #1 models

> hide #2 models

> hide #3 models

> hide #4 models

Alignment identifier is 1  

> select #1/A:1 #2/A:1 #3/A:1 #4/A:1 #5/A:1

40 atoms, 35 bonds, 5 residues, 5 models selected  

> select #1/A #2/A #3/A #4/A #5/A

26575 atoms, 27070 bonds, 3335 residues, 5 models selected  
1 [ID: 1] region 5 chains [1-667] RMSD: 46.419  
  

> show #4 models

> show #3 models

> show #2 models

> show #1 models

> ui tool show Matchmaker

> matchmaker #1-4 to #5

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 PUS7L_af5cb_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#5) with
PUS7L_af5cb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#1), sequence alignment score = 3367.4  
RMSD between 483 pruned atom pairs is 0.396 angstroms; (across all 667 pairs:
8.753)  
  
Matchmaker PUS7L_af5cb_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#5) with
PUS7L_af5cb_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#2), sequence alignment score = 3313.4  
RMSD between 486 pruned atom pairs is 0.759 angstroms; (across all 667 pairs:
5.937)  
  
Matchmaker PUS7L_af5cb_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#5) with
PUS7L_af5cb_unrelaxed_rank_003_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#3), sequence alignment score = 3354.8  
RMSD between 530 pruned atom pairs is 0.653 angstroms; (across all 667 pairs:
6.398)  
  
Matchmaker PUS7L_af5cb_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#5) with
PUS7L_af5cb_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb, chain A
(#4), sequence alignment score = 3365.6  
RMSD between 540 pruned atom pairs is 0.620 angstroms; (across all 667 pairs:
7.541)  
  

> matchmaker #1-4 to #5

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 PUS7L_af5cb_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#5) with
PUS7L_af5cb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#1), sequence alignment score = 3367.4  
RMSD between 483 pruned atom pairs is 0.396 angstroms; (across all 667 pairs:
8.753)  
  
Matchmaker PUS7L_af5cb_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#5) with
PUS7L_af5cb_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#2), sequence alignment score = 3313.4  
RMSD between 486 pruned atom pairs is 0.759 angstroms; (across all 667 pairs:
5.937)  
  
Matchmaker PUS7L_af5cb_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#5) with
PUS7L_af5cb_unrelaxed_rank_003_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#3), sequence alignment score = 3354.8  
RMSD between 530 pruned atom pairs is 0.653 angstroms; (across all 667 pairs:
6.398)  
  
Matchmaker PUS7L_af5cb_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#5) with
PUS7L_af5cb_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb, chain A
(#4), sequence alignment score = 3365.6  
RMSD between 540 pruned atom pairs is 0.620 angstroms; (across all 667 pairs:
7.541)  
  

> select #1/A:667 #2/A:667 #3/A:667 #4/A:667 #5/A:667

55 atoms, 50 bonds, 5 residues, 5 models selected  

> select #1/A:667 #2/A:667 #3/A:667 #4/A:667 #5/A:667

55 atoms, 50 bonds, 5 residues, 5 models selected  
1 [ID: 1] region 5 chains [667] RMSD: 10.101  
  

> save "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold predictions/Top 5 full-
> length PUS7L structures overlayed .cxs"

——— End of log from Thu Mar 16 13:39:25 2023 ———

opened ChimeraX session  

> select
> #1/A:91-107,111-114,134-136,165-170,173-183,185-187,201-214,239-247,275-286,290-292,316-324,362-374,383-386,393-401,405-413,422-434,437-443,450-461,466-472,475-501,522-527,530-532,548-560,572-574,608-612,641-649,655-666
> #2/A:91-107,111-114,134-136,165-170,173-183,185-187,201-214,239-247,275-286,290-292,316-324,362-374,383-386,393-401,405-413,422-434,437-443,450-461,466-472,475-501,522-527,530-532,548-560,572-574,608-612,641-649,655-666
> #3/A:91-107,111-114,134-136,165-170,173-183,185-187,201-214,239-247,275-286,290-292,316-324,362-374,383-386,393-401,405-413,422-434,437-443,450-461,466-472,475-501,522-527,530-532,548-560,572-574,608-612,641-649,655-666
> #4/A:91-107,111-114,134-136,165-170,173-183,185-187,201-214,239-247,275-286,290-292,316-324,362-374,383-386,393-401,405-413,422-434,437-443,450-461,466-472,475-501,522-527,530-532,548-560,572-574,608-612,641-649,655-666
> #5/A:91-107,111-114,134-136,165-170,173-183,185-187,201-214,239-247,275-286,290-292,316-324,362-374,383-386,393-401,405-413,422-434,437-443,450-461,466-472,475-501,522-527,530-532,548-560,572-574,608-612,641-649,655-666

10030 atoms, 10050 bonds, 1215 residues, 5 models selected  

> select #1/A:244 #2/A:244 #3/A:244 #4/A:244 #5/A:244

45 atoms, 40 bonds, 5 residues, 5 models selected  

> select #1/A:244-250 #2/A:244-250 #3/A:244-250 #4/A:244-250 #5/A:244-250

260 atoms, 255 bonds, 35 residues, 5 models selected  
1 [ID: 1] region 5 chains [244-250] RMSD: 9.860  
  

> close session

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7S_homo_c2fac/PUS7S_homo_c2fac_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"

Chain information for
PUS7S_homo_c2fac_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7S_homo_c2fac/PUS7S_homo_c2fac_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb"

Chain information for
PUS7S_homo_c2fac_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7S_homo_c2fac/PUS7S_homo_c2fac_unrelaxed_rank_003_alphafold2_ptm_model_5_seed_000.pdb"

Chain information for
PUS7S_homo_c2fac_unrelaxed_rank_003_alphafold2_ptm_model_5_seed_000.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7S_homo_c2fac/PUS7S_homo_c2fac_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb"

Chain information for
PUS7S_homo_c2fac_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7S_homo_c2fac/PUS7S_homo_c2fac_unrelaxed_rank_005_alphafold2_ptm_model_2_seed_000.pdb"

Chain information for
PUS7S_homo_c2fac_unrelaxed_rank_005_alphafold2_ptm_model_2_seed_000.pdb #5  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #2-5 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
PUS7S_homo_c2fac_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain
A (#1) with
PUS7S_homo_c2fac_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb, chain
A (#2), sequence alignment score = 3344.9  
RMSD between 489 pruned atom pairs is 0.456 angstroms; (across all 661 pairs:
10.151)  
  
Matchmaker
PUS7S_homo_c2fac_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain
A (#1) with
PUS7S_homo_c2fac_unrelaxed_rank_003_alphafold2_ptm_model_5_seed_000.pdb, chain
A (#3), sequence alignment score = 3343.7  
RMSD between 467 pruned atom pairs is 0.533 angstroms; (across all 661 pairs:
12.826)  
  
Matchmaker
PUS7S_homo_c2fac_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain
A (#1) with
PUS7S_homo_c2fac_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb, chain
A (#4), sequence alignment score = 3340.7  
RMSD between 556 pruned atom pairs is 0.645 angstroms; (across all 661 pairs:
13.432)  
  
Matchmaker
PUS7S_homo_c2fac_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain
A (#1) with
PUS7S_homo_c2fac_unrelaxed_rank_005_alphafold2_ptm_model_2_seed_000.pdb, chain
A (#5), sequence alignment score = 3338.3  
RMSD between 487 pruned atom pairs is 0.402 angstroms; (across all 661 pairs:
14.550)  
  

> close session

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7S_homo_c2fac/PUS7S_homo_c2fac_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"

Chain information for
PUS7S_homo_c2fac_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7L_af5cb_FullHumanPUS7L
> structure/PUS7L_af5cb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"

Chain information for
PUS7L_af5cb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #2  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> 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
PUS7S_homo_c2fac_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain
A (#1) with
PUS7L_af5cb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#2), sequence alignment score = 3360.6  
RMSD between 481 pruned atom pairs is 0.271 angstroms; (across all 661 pairs:
11.114)  
  

> ui tool show Matchmaker

> matchmaker #2 to #1/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
PUS7S_homo_c2fac_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain
A (#1) with
PUS7L_af5cb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#2), sequence alignment score = 3360.6  
RMSD between 481 pruned atom pairs is 0.271 angstroms; (across all 661 pairs:
11.114)  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7L_af5cb_FullHumanPUS7L
> structure/PUS7L_af5cb_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000.pdb"

Chain information for
PUS7L_af5cb_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7L_af5cb_FullHumanPUS7L
> structure/PUS7L_af5cb_unrelaxed_rank_003_alphafold2_ptm_model_4_seed_000.pdb"

Chain information for
PUS7L_af5cb_unrelaxed_rank_003_alphafold2_ptm_model_4_seed_000.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7L_af5cb_FullHumanPUS7L
> structure/PUS7L_af5cb_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb"

Chain information for
PUS7L_af5cb_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb #5  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7L_af5cb_FullHumanPUS7L
> structure/PUS7L_af5cb_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb"

Chain information for
PUS7L_af5cb_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb #6  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7S_homo_c2fac/PUS7S_homo_c2fac_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb"

Chain information for
PUS7S_homo_c2fac_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb #7  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7S_homo_c2fac/PUS7S_homo_c2fac_unrelaxed_rank_003_alphafold2_ptm_model_5_seed_000.pdb"

Chain information for
PUS7S_homo_c2fac_unrelaxed_rank_003_alphafold2_ptm_model_5_seed_000.pdb #8  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7S_homo_c2fac/PUS7S_homo_c2fac_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb"

Chain information for
PUS7S_homo_c2fac_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb #9  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7S_homo_c2fac/PUS7S_homo_c2fac_unrelaxed_rank_005_alphafold2_ptm_model_2_seed_000.pdb"

Chain information for
PUS7S_homo_c2fac_unrelaxed_rank_005_alphafold2_ptm_model_2_seed_000.pdb #10  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #2-6 & sel to #1/A pairing bs

No molecules/chains to match specified  
No reference and/or match structure/chain chosen  

> matchmaker #2-6 & sel to #1/A & sel pairing bs

No 'to' chains specified  

> matchmaker #1/A#1/A#1/A#1/A#1/A & sel to #2/A#3/A#4/A#5/A#6/A & sel pairing
> ss

No 'to' chains specified  

> matchmaker #2-10 & sel to #1 & sel

No 'to' model specified  

> close session

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7L_af5cb_FullHumanPUS7L
> structure/PUS7L_af5cb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"

Chain information for
PUS7L_af5cb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7S_homo_c2fac/PUS7S_homo_c2fac_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"

Chain information for
PUS7S_homo_c2fac_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7S_homo_c2fac/PUS7S_homo_c2fac_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb"

Chain information for
PUS7S_homo_c2fac_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7S_homo_c2fac/PUS7S_homo_c2fac_unrelaxed_rank_003_alphafold2_ptm_model_5_seed_000.pdb"

Chain information for
PUS7S_homo_c2fac_unrelaxed_rank_003_alphafold2_ptm_model_5_seed_000.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7S_homo_c2fac/PUS7S_homo_c2fac_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb"

Chain information for
PUS7S_homo_c2fac_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb #5  
---  
Chain | Description  
A | No description available  
  

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7S_homo_c2fac/PUS7S_homo_c2fac_unrelaxed_rank_005_alphafold2_ptm_model_2_seed_000.pdb"

Chain information for
PUS7S_homo_c2fac_unrelaxed_rank_005_alphafold2_ptm_model_2_seed_000.pdb #6  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #2-6 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 PUS7L_af5cb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
PUS7S_homo_c2fac_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain
A (#2), sequence alignment score = 3360.6  
RMSD between 481 pruned atom pairs is 0.271 angstroms; (across all 661 pairs:
11.114)  
  
Matchmaker PUS7L_af5cb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
PUS7S_homo_c2fac_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb, chain
A (#3), sequence alignment score = 3339.6  
RMSD between 473 pruned atom pairs is 0.562 angstroms; (across all 661 pairs:
9.405)  
  
Matchmaker PUS7L_af5cb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
PUS7S_homo_c2fac_unrelaxed_rank_003_alphafold2_ptm_model_5_seed_000.pdb, chain
A (#4), sequence alignment score = 3338.4  
RMSD between 464 pruned atom pairs is 0.615 angstroms; (across all 661 pairs:
7.711)  
  
Matchmaker PUS7L_af5cb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
PUS7S_homo_c2fac_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb, chain
A (#5), sequence alignment score = 3322.8  
RMSD between 478 pruned atom pairs is 0.370 angstroms; (across all 661 pairs:
8.738)  
  
Matchmaker PUS7L_af5cb_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#1) with
PUS7S_homo_c2fac_unrelaxed_rank_005_alphafold2_ptm_model_2_seed_000.pdb, chain
A (#6), sequence alignment score = 3330  
RMSD between 481 pruned atom pairs is 0.383 angstroms; (across all 661 pairs:
9.048)  
  

> hide #1 models

> show #1 models

> hide #1 models

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7L_af5cb_FullHumanPUS7L
> structure/PUS7L_af5cb_scores_rank_002_alphafold2_ptm_model_5_seed_000.json"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 51, in event  
if self.handle_drag_and_drop(event):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 116, in handle_drag_and_drop  
mw.dropEvent(event)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 559, in dropEvent  
_open_dropped_file(self.session, p)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1922, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mole/__init__.py", line 27, in open  
return mole.read_mole_json(session, data, file_name, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mole/mole.py", line 40, in read_mole_json  
models = channel_models(session, j['Channels'], transparency/100.0)  
KeyError: 'Channels'  
  
KeyError: 'Channels'  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mole/mole.py", line 40, in read_mole_json  
models = channel_models(session, j['Channels'], transparency/100.0)  
  
See log for complete Python traceback.  
  

> close session

> open "/Users/murnj/Dropbox/Murn lab/PUS7/Alfafold
> predictions/PUS7L_af5cb_FullHumanPUS7L
> structure/PUS7L_af5cb_scores_rank_002_alphafold2_ptm_model_5_seed_000.json"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 559, in dropEvent  
_open_dropped_file(self.session, p)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1922, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mole/__init__.py", line 27, in open  
return mole.read_mole_json(session, data, file_name, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mole/mole.py", line 40, in read_mole_json  
models = channel_models(session, j['Channels'], transparency/100.0)  
KeyError: 'Channels'  
  
KeyError: 'Channels'  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mole/mole.py", line 40, in read_mole_json  
models = channel_models(session, j['Channels'], transparency/100.0)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 575 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
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: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 4.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 522.0.0.0.0
      OS Loader Version: 577.140.2~15
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 13.6.1 (22G313)
      Kernel Version: Darwin 22.6.0
      Time since boot: 13 days, 23 hours, 2 minutes

Graphics/Displays:

    Radeon Pro 575:

      Chipset Model: Radeon Pro 575
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c4
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1P-025
      EFI Driver Version: 01.00.931
      Metal Support: Metal 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    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: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0