id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9352 Matchmaker failure johannes_walter@… Eric Pettersen "{{{ 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 }}} " defect closed normal Structure Comparison not a bug all ChimeraX