Opened 2 years ago

Closed 2 years ago

Last modified 2 years ago

#9352 closed defect (not a bug)

Matchmaker failure

Reported by: johannes_walter@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Comparison Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-12.6.6-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
I am finding that the matchmaker function is not working properly to align related structures (5 highly related models of a tetrameric complex generated by AlphaFold). One of the models will not align with the others, even though it's clearly almost identical. Thanks for your help. JW

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

> open "/Users/johannes/Dropbox (HMS)/A To do/2023-07-25 DONSON
> revision/Figures and tables/Figure SX (GINS-TOPBP1 interaction)/GINS-TOPBP1
> Human .cxs"

Log from Tue Jul 11 09:45:33 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/johannes/Dropbox (HMS)/A To do/2023-07-25 DONSON
> revision/Figures and tables/Figure SX (GINS-TOPBP1)/GINS-TOPBP1 Human .cxs"

Log from Mon Jul 10 22:43:26 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/johannes/Dropbox (HMS)/Alphafold/AlphaFold
> Jobs/remote_job_0000237_walter (hGINS-hTOPB1)/TOPB1_HUMAN__PSF1_HUMAN-
> PSF2_HUMAN-PSF3_HUMAN-
> SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb"

Chain information for TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> open "/Users/johannes/Dropbox (HMS)/Alphafold/AlphaFold
> Jobs/remote_job_0000237_walter (hGINS-hTOPB1)/TOPB1_HUMAN__PSF1_HUMAN-
> PSF2_HUMAN-PSF3_HUMAN-
> SLD5_HUMAN__2342aa_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_000.pdb"

Chain information for TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_000.pdb
#2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> open "/Users/johannes/Dropbox (HMS)/Alphafold/AlphaFold
> Jobs/remote_job_0000237_walter (hGINS-hTOPB1)/TOPB1_HUMAN__PSF1_HUMAN-
> PSF2_HUMAN-PSF3_HUMAN-
> SLD5_HUMAN__2342aa_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb"

Chain information for TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb
#3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> open "/Users/johannes/Dropbox (HMS)/Alphafold/AlphaFold
> Jobs/remote_job_0000237_walter (hGINS-hTOPB1)/TOPB1_HUMAN__PSF1_HUMAN-
> PSF2_HUMAN-PSF3_HUMAN-
> SLD5_HUMAN__2342aa_unrelaxed_rank_004_alphafold2_multimer_v3_model_3_seed_000.pdb"

Chain information for TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_004_alphafold2_multimer_v3_model_3_seed_000.pdb
#4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> open "/Users/johannes/Dropbox (HMS)/Alphafold/AlphaFold
> Jobs/remote_job_0000237_walter (hGINS-hTOPB1)/TOPB1_HUMAN__PSF1_HUMAN-
> PSF2_HUMAN-PSF3_HUMAN-
> SLD5_HUMAN__2342aa_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb"

Chain information for TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb
#5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | 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 TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#1) with TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain A (#2), sequence alignment score = 7528.2  
RMSD between 195 pruned atom pairs is 0.331 angstroms; (across all 1522 pairs:
36.876)  
  

> ui tool show Matchmaker

> 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 TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#1) with TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#3), sequence alignment score = 7456.8  
RMSD between 200 pruned atom pairs is 0.327 angstroms; (across all 1522 pairs:
83.873)  
  

> ui tool show Matchmaker

> 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 TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#1) with TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_004_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain A (#4), sequence alignment score = 7353.6  
RMSD between 166 pruned atom pairs is 0.437 angstroms; (across all 1522 pairs:
59.516)  
  

> ui tool show Matchmaker

> matchmaker #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 TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#1) with TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#5), sequence alignment score = 7440  
RMSD between 271 pruned atom pairs is 0.363 angstroms; (across all 1522 pairs:
66.647)  
  

> save "/Users/johannes/Dropbox (HMS)/A To do/2023-07-25 DONSON
> revision/Figures and tables/Figure SX (GINS-TOPBP1)/GINS-TOPBP1 Human .cxs"

> select #1-5/A:1-473

18945 atoms, 19345 bonds, 2365 residues, 5 models selected  

> hide sel target a

> select #1-5/A:764-1550

29840 atoms, 30470 bonds, 3795 residues, 5 models selected  

> hide sel atoms

> select #1-5/A:511-540

1160 atoms, 1185 bonds, 150 residues, 5 models selected  

> hide sel atoms

> select #1-5/B-E

33345 atoms, 34015 bonds, 4100 residues, 5 models selected  

> hide sel atoms

> show sel surfaces

> color (#!1-5 & sel) cyan

> hide sel atoms

> select #1-5/A

59950 atoms, 61185 bonds, 7610 residues, 5 models selected  

> hide sel atoms

> show sel cartoons

> select #1-5/A:1-473

18945 atoms, 19345 bonds, 2365 residues, 5 models selected  

> hide sel cartoons

> select #1-5/A:764-1600

29840 atoms, 30470 bonds, 3795 residues, 5 models selected  

> hide sel cartoons

> select #1-5/A:511-540

1160 atoms, 1185 bonds, 150 residues, 5 models selected  

> hide sel cartoons

> 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 TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#1) with TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain A (#2), sequence alignment score = 7528.2  
RMSD between 195 pruned atom pairs is 0.331 angstroms; (across all 1522 pairs:
36.876)  
  

> ui tool show Matchmaker

> 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 TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#1) with TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#3), sequence alignment score = 7456.8  
RMSD between 200 pruned atom pairs is 0.327 angstroms; (across all 1522 pairs:
83.873)  
  

> ui tool show Matchmaker

> 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 TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#1) with TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_004_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain A (#4), sequence alignment score = 7353.6  
RMSD between 166 pruned atom pairs is 0.437 angstroms; (across all 1522 pairs:
59.516)  
  

> 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 TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#1) with TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain A (#2), sequence alignment score = 7528.2  
RMSD between 195 pruned atom pairs is 0.331 angstroms; (across all 1522 pairs:
36.876)  
  

> ui tool show Matchmaker

> 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 TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#1) with TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#3), sequence alignment score = 7456.8  
RMSD between 200 pruned atom pairs is 0.327 angstroms; (across all 1522 pairs:
83.873)  
  

> ui tool show Matchmaker

> 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 TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#1) with TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_004_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain A (#4), sequence alignment score = 7353.6  
RMSD between 166 pruned atom pairs is 0.437 angstroms; (across all 1522 pairs:
59.516)  
  

> ui tool show Matchmaker

> matchmaker #!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 TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#1) with TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#5), sequence alignment score = 7440  
RMSD between 271 pruned atom pairs is 0.363 angstroms; (across all 1522 pairs:
66.647)  
  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> ui tool show Matchmaker

> matchmaker #!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 TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#1) with TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#5), sequence alignment score = 7440  
RMSD between 271 pruned atom pairs is 0.363 angstroms; (across all 1522 pairs:
66.647)  
  

> hide #!5 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> ui tool show Matchmaker

> matchmaker #2/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#1) with TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain A (#2), sequence alignment score = 7528.2  
RMSD between 195 pruned atom pairs is 0.331 angstroms; (across all 1522 pairs:
36.876)  
  

> ui tool show Matchmaker

> matchmaker #3/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#1) with TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#3), sequence alignment score = 7456.8  
RMSD between 200 pruned atom pairs is 0.327 angstroms; (across all 1522 pairs:
83.873)  
  

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> ui tool show Matchmaker

> matchmaker #4/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#1) with TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_004_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain A (#4), sequence alignment score = 7353.6  
RMSD between 166 pruned atom pairs is 0.437 angstroms; (across all 1522 pairs:
59.516)  
  

> ui tool show Matchmaker

> matchmaker #5/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#1) with TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#5), sequence alignment score = 7440  
RMSD between 271 pruned atom pairs is 0.363 angstroms; (across all 1522 pairs:
66.647)  
  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!5 models

> hide #!4 models

> show #!4 models

> show #!3 models

> save "/Users/johannes/Dropbox (HMS)/A To do/2023-07-25 DONSON
> revision/Figures and tables/Figure SX (GINS-TOPBP1)/GINS-TOPBP1 Human .cxs"

——— End of log from Mon Jul 10 22:43:26 2023 ———

opened ChimeraX session  

> hide #!4 models

> hide #!3 models

> show #!1 models

> log metadata #1

No models had metadata

> log chains #1

Chain information for TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> select #1/A

11990 atoms, 12237 bonds, 1522 residues, 1 model selected  

> select #1/A:475-479

40 atoms, 41 bonds, 5 residues, 1 model selected  

> select #1/A:474-479

49 atoms, 50 bonds, 6 residues, 1 model selected  

> select #1/A:474-478

42 atoms, 42 bonds, 5 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/A:498-510

94 atoms, 93 bonds, 13 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/A:497-510

4 atoms, 3 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/A:743-800

464 atoms, 470 bonds, 58 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/A:541-548

57 atoms, 57 bonds, 8 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/E:1-14

106 atoms, 106 bonds, 14 residues, 1 model selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> select #1/A

11329 atoms, 11563 bonds, 4 pseudobonds, 1437 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel gold

> select #1/B-E

6563 atoms, 6696 bonds, 806 residues, 1 model selected  

> color sel sky blue

[Repeated 1 time(s)]

> set bgColor white

> select clear

> save "/Users/johannes/Dropbox (HMS)/A To do/2023-07-25 DONSON
> revision/Figures and tables/Figure SX (GINS-TOPBP1)/GINS-TOPBP1 Human .cxs"

> open 7PLO

7plo title:  
H. sapiens replisome-CUL2/LRR1 complex [more info...]  
  
Chain information for 7plo #6  
---  
Chain | Description | UniProt  
2 | DNA replication licensing factor MCM2 | MCM2_HUMAN  
3 | DNA replication licensing factor MCM3 | MCM3_HUMAN  
4 | DNA replication licensing factor MCM4 | MCM4_HUMAN  
5 | DNA replication licensing factor MCM5 | MCM5_HUMAN  
6 | DNA replication licensing factor MCM6 | MCM6_HUMAN  
7 | DNA replication licensing factor MCM7 | MCM7_HUMAN  
A | DNA polymerase epsilon subunit 2 | DPOE2_HUMAN  
B | DNA polymerase epsilon catalytic subunit A | DPOE1_HUMAN  
C | Cell division control protein 45 homolog | CDC45_HUMAN  
D | DNA replication complex GINS protein PSF1 | PSF1_HUMAN  
E | DNA replication complex GINS protein PSF2 | PSF2_HUMAN  
F | DNA replication complex GINS protein PSF3 | PSF3_HUMAN  
G | DNA replication complex GINS protein SLD5 | SLD5_HUMAN  
H I J | WD repeat and HMG-box DNA-binding protein 1 | WDHD1_HUMAN  
K | Protein timeless homolog | TIM_HUMAN  
L | TIMELESS-interacting protein | TIPIN_HUMAN  
M | Leading strand DNA |  
N | Lagging strand DNA |  
O | Leucine-rich repeat protein 1 | LLR1_HUMAN  
P | Elongin-B | ELOB_HUMAN  
Q | Claspin | CLSPN_HUMAN  
R | Elongin-C | ELOC_HUMAN  
S | Cullin-2 | CUL2_HUMAN  
T | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN  
  
Non-standard residues in 7plo #6  
---  
ANP — phosphoaminophosphonic acid-adenylate ester  
MG — magnesium ion  
SO4 — sulfate ion  
ZN — zinc ion  
  

> log metadata #6

Metadata for 7plo #6  
---  
Title | H. sapiens replisome-CUL2/LRR1 complex  
Citation | Jenkyn-Bedford, M., Jones, M.L., Baris, Y., Labib, K.P.M., Cannone,
G., Yeeles, J.T.P., Deegan, T.D. (2021). A conserved mechanism for regulating
replisome disassembly in eukaryotes. Nature, 600, 743-747. PMID: 34700328.
DOI: 10.1038/s41586-021-04145-3  
Non-standard residues | ANP — phosphoaminophosphonic acid-adenylate ester  
MG — magnesium ion  
SO4 — sulfate ion  
ZN — zinc ion  
Gene source | Homo sapiens (human)  
CryoEM Map | EMDB 13494 — open map  
Experimental method | Electron microscopy  
Resolution | 2.8Å  
  
> log chains #6

Chain information for 7plo #6  
---  
Chain | Description | UniProt  
2 | DNA replication licensing factor MCM2 | MCM2_HUMAN  
3 | DNA replication licensing factor MCM3 | MCM3_HUMAN  
4 | DNA replication licensing factor MCM4 | MCM4_HUMAN  
5 | DNA replication licensing factor MCM5 | MCM5_HUMAN  
6 | DNA replication licensing factor MCM6 | MCM6_HUMAN  
7 | DNA replication licensing factor MCM7 | MCM7_HUMAN  
A | DNA polymerase epsilon subunit 2 | DPOE2_HUMAN  
B | DNA polymerase epsilon catalytic subunit A | DPOE1_HUMAN  
C | Cell division control protein 45 homolog | CDC45_HUMAN  
D | DNA replication complex GINS protein PSF1 | PSF1_HUMAN  
E | DNA replication complex GINS protein PSF2 | PSF2_HUMAN  
F | DNA replication complex GINS protein PSF3 | PSF3_HUMAN  
G | DNA replication complex GINS protein SLD5 | SLD5_HUMAN  
H I J | WD repeat and HMG-box DNA-binding protein 1 | WDHD1_HUMAN  
K | Protein timeless homolog | TIM_HUMAN  
L | TIMELESS-interacting protein | TIPIN_HUMAN  
M | Leading strand DNA |  
N | Lagging strand DNA |  
O | Leucine-rich repeat protein 1 | LLR1_HUMAN  
P | Elongin-B | ELOB_HUMAN  
Q | Claspin | CLSPN_HUMAN  
R | Elongin-C | ELOC_HUMAN  
S | Cullin-2 | CUL2_HUMAN  
T | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN  
  

> select #6/2-7

30086 atoms, 30575 bonds, 42 pseudobonds, 3807 residues, 3 models selected  

> hide sel atoms

> select #6

78820 atoms, 80416 bonds, 143 pseudobonds, 9825 residues, 4 models selected  

> hide sel atoms

> select #6/A-G

20867 atoms, 21317 bonds, 18 pseudobonds, 2591 residues, 3 models selected  

> show sel cartoons

> ui tool show Matchmaker

> matchmaker #!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 TOPB1_HUMAN__PSF1_HUMAN-PSF2_HUMAN-PSF3_HUMAN-
SLD5_HUMAN__2342aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain E (#1) with 7plo, chain G (#6), sequence alignment score = 1033.9  
RMSD between 203 pruned atom pairs is 0.325 angstroms; (across all 203 pairs:
0.325)  
  

> select #6/A

4200 atoms, 4310 bonds, 528 residues, 1 model selected  

> select #6/C

4347 atoms, 4439 bonds, 1 pseudobond, 534 residues, 2 models selected  

> hide sel cartoons

> select #6/B

6051 atoms, 6170 bonds, 16 pseudobonds, 760 residues, 3 models selected  

> hide sel cartoons

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!1 models

> show #!1 models

> select #1/BE

Nothing selected  

> select #1/B-E

6563 atoms, 6696 bonds, 806 residues, 1 model selected  

> hide sel surfaces

> show sel cartoons

> select clear

> select #1/B-E

6563 atoms, 6696 bonds, 806 residues, 1 model selected  

> hide sel cartoons

> show sel surfaces

> select #6/D-G

6269 atoms, 6398 bonds, 1 pseudobond, 769 residues, 2 models selected  

> hide sel cartoons

> hide #!6 models

> show #!6 models

> hide #!6 models

> save "/Users/johannes/Dropbox (HMS)/A To do/2023-07-25 DONSON
> revision/Figures and tables/Figure SX (GINS-TOPBP1)/GINS-TOPBP1 Human .cxs"

> save "/Users/johannes/Dropbox (HMS)/A To do/2023-07-25 DONSON
> revision/Figures and tables/Figure SX (GINS-TOPBP1 interaction)/GINS-TOPBP1
> Human .cxs"

> save /Users/johannes/Desktop/TOPBP1-GINS.png width 1992 height 1132
> supersample 3 transparentBackground true

> show #!6 models

> save /Users/johannes/Desktop/TOPBP1-GINS-POLE2.png width 1992 height 1132
> supersample 3 transparentBackground true

> open "/Users/johannes/Dropbox (HMS)/Alphafold/AlphaFold
> Jobs/remote_job_0000239_walter (xlGINS-xlTOPBP1)/TOB1A_XENLA__PSF1_XENLA-
> PSF2_XENLA-PSF3_XENLA-
> SLD5_XENLA__2325aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"

Chain information for TOB1A_XENLA__PSF1_XENLA-PSF2_XENLA-PSF3_XENLA-
SLD5_XENLA__2325aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> select #7/A

11884 atoms, 12129 bonds, 1513 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #7/B-E

6597 atoms, 6732 bonds, 812 residues, 1 model selected  

> hide sel atoms

> show sel surfaces

> ui tool show Matchmaker

> save "/Users/johannes/Dropbox (HMS)/A To do/2023-07-25 DONSON
> revision/Figures and tables/Figure SX (GINS-TOPBP1 interaction)/GINS-TOPBP1
> Human .cxs"

——— End of log from Tue Jul 11 09:45:33 2023 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple

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: Mac mini
      Model Identifier: Macmini9,1
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 8422.121.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.6.6 (21G646)
      Kernel Version: Darwin 21.6.0
      Time since boot: 3 days 16:42

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        LG HDR DQHD:
          Resolution: 5120 x 1440
          UI Looks like: 5120 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


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

Change History (5)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Structure Comparison
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Matchmaker failure

comment:2 by Eric Pettersen, 2 years ago

Status: accepted → feedback

Hi Johannes,

Thanks for reporting this problem. Looking through the log in your report, I don't see any MatchMaker commands that produced particularly low numbers of matched atoms or particularly high RMSD values. Could you provide an example of structures that aren't being matched?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by johannes_walter@…, 2 years ago 

Hi Eric,
Thanks for the rapid reply.
The problem was I was aligning AlphaFold structures with a lot of disordered sequence.
When I aligned on a well-ordered subunit, alignment worked well.
Another question, how do I delete or hide the dotted lines that connect parts of proteins where intervening residues have been deleted?
I really appreciate your time. ChimeraX is so much easier to use than pymol!
Thanks
Johannes


From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Tuesday, July 11, 2023 at 12:34 PM
To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>, Walter, Johannes <johannes_walter@hms.harvard.edu>
Subject: Re: [ChimeraX] #9352: Matchmaker failure
#9352: Matchmaker failure
-------------------------------------------+----------------------
          Reporter:  johannes_walter@…     |      Owner:  pett
              Type:  defect                |     Status:  feedback
          Priority:  normal                |  Milestone:
         Component:  Structure Comparison  |    Version:
        Resolution:                        |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+----------------------
Changes (by pett):

 * status:  accepted => feedback

Comment:

 Hi Johannes,
         Thanks for reporting this problem.  Looking through the log in
 your report, I don't see any MatchMaker commands that produced
 particularly low numbers of matched atoms or particularly high RMSD
 values.  Could you provide an example of structures that aren't being
 matched?

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9352#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:4 by Eric Pettersen, 2 years ago

Resolution: → not a bug
Status: feedback → closed

Hi Johannes,

If you need to get MatchMaker to basically ignore the disordered regions, you could select the well-ordered regions and then tell MatchMaker to restrict the matching to the selection, as described here: ​https://www.cgl.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#restrict
To hide the missing-structure pseudobonds that you're describing, in the Model Panel click the disclosure triangle next to the structure with the pseudobonds to reveal associated submodels. One of them should be named "missing structure". You can use the check button under the "eyeball" icon to hide it.

--Eric

comment:5 by johannes_walter@…, 2 years ago 

Fantastic, thanks!

From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Tuesday, July 11, 2023 at 2:39 PM
To: Walter, Johannes <johannes_walter@hms.harvard.edu>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #9352: Matchmaker failure
#9352: Matchmaker failure
-------------------------------------------+--------------------
          Reporter:  johannes_walter@…     |      Owner:  pett
              Type:  defect                |     Status:  closed
          Priority:  normal                |  Milestone:
         Component:  Structure Comparison  |    Version:
        Resolution:  not a bug             |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+--------------------
Changes (by pett):

 * resolution:   => not a bug
 * status:  feedback => closed

Comment:

 Hi Johannes,
         If you need to get MatchMaker to basically ignore the disordered
 regions, you could select the well-ordered regions and then tell
 MatchMaker to restrict the matching to the selection, as described here:
 https://www.cgl.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#restrict
         To hide the missing-structure pseudobonds that you're describing,
 in the Model Panel click the disclosure triangle next to the structure
 with the pseudobonds to reveal associated submodels.  One of them should
 be named "missing structure".  You can use the check button under the
 "eyeball" icon to hide it.

 --Eric
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9352#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
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