id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9078 "AlphaFold sequence search web service failed (500) ""Internal Server Error""" santiago.jus.are@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22621 ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description When I execute the command: ""alphafold match ......."". I get this error: AlphaFold sequence search web service failed (500) ""Internal Server Error"" https://www.rbvi.ucsf.edu/chimerax/cgi-bin/alphafold_search3_cgi.py However, few weeks ago I took the same sequence using the same command. Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open ""I:\\\Mi > unidad\\\Santiago\\\BIO_INF_TEC_URP\\\Bacillus\\\Resultados\\\Bioinf\\\Tesis_David\\\id_char_muts\\\par1_vs_CynD.cxs"" Log from Sun Apr 30 21:29:43 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open ""I:/Mi > unidad/Santiago/BIO_INF_TEC_URP/Bacillus/Resultados/Bioinf/Tesis_David/id_char_muts/par2_vs_CynD.cxs"" Log from Sun Apr 30 01:02:17 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show AlphaFold No sequence chosen for AlphaFold match Fetching A0A1D7XF17 UniProt info from https://www.uniprot.org/uniprot/A0A1D7XF17.xml > alphafold match A0A1D7XF17 Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json 1 UniProt id does not have an AlphaFold database model: A0A1D7XF17 (UniProt A0A1D7XF17) Fetching compressed AlphaFold A0A1D7XF17 from https://alphafold.ebi.ac.uk/files/AF-A0A1D7XF17-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A1D7XF17 (UniProt A0A1D7XF17) Opened 1 AlphaFold model Fetching U7U7F7 UniProt info from https://www.uniprot.org/uniprot/U7U7F7.xml > alphafold match U7U7F7 1 UniProt id does not have an AlphaFold database model: U7U7F7 (UniProt U7U7F7) Fetching compressed AlphaFold U7U7F7 from https://alphafold.ebi.ac.uk/files/AF-U7U7F7-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: U7U7F7 (UniProt U7U7F7) Opened 1 AlphaFold model > mmaker #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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold U7U7F7_9BURK, chain A (#2), sequence alignment score = 767 RMSD between 256 pruned atom pairs is 0.740 angstroms; (across all 325 pairs: 13.043) > mmaker #2 to #1 showAlignment true 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold U7U7F7_9BURK, chain A (#2), sequence alignment score = 767 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: AlphaFold A0A1D7XF17_ALCSP #1/A, AlphaFold U7U7F7_9BURK #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 256 pruned atom pairs is 0.740 angstroms; (across all 325 pairs: 13.043) > select #1/A:229 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/A:229-237 #2/A:240-248 146 atoms, 148 bonds, 18 residues, 2 models selected MatchMaker Alignment [ID: 1] region AlphaFold A0A1D7XF17_ALCSP, chain A..AlphaFold U7U7F7_9BURK, chain A [241-249] RMSD: 4.627 > select #1/A:293 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:293-300 64 atoms, 66 bonds, 8 residues, 1 model selected Fetching A3LPM9 UniProt info from https://www.uniprot.org/uniprot/A3LPM9.xml > alphafold match A3LPM9 1 UniProt id does not have an AlphaFold database model: A3LPM9 (UniProt A3LPM9) Fetching compressed AlphaFold A3LPM9 from https://alphafold.ebi.ac.uk/files/AF-A3LPM9-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A3LPM9 (UniProt A3LPM9) Opened 1 AlphaFold model Fetching A8FEX8 UniProt info from https://www.uniprot.org/uniprot/A8FEX8.xml > alphafold match A8FEX8 1 UniProt id does not have an AlphaFold database model: A8FEX8 (UniProt A8FEX8) Fetching compressed AlphaFold A8FEX8 from https://alphafold.ebi.ac.uk/files/AF-A8FEX8-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A8FEX8 (UniProt A8FEX8) Opened 1 AlphaFold model > mmaker #3 to #1 showAlignment true 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold A3LPM9_PICST, chain A (#3), sequence alignment score = 1365.7 Alignment identifier is 2 Showing conservation header (""seq_conservation"" residue attribute) for alignment 2 Hiding conservation header for alignment 2 Chains used in RMSD evaluation for alignment 2: AlphaFold A0A1D7XF17_ALCSP #1/A, AlphaFold A3LPM9_PICST #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2 RMSD between 260 pruned atom pairs is 0.454 angstroms; (across all 324 pairs: 15.791) > mmaker #4 to #1 showAlignment true 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold A8FEX8_BACP2, chain A (#4), sequence alignment score = 1458.2 Alignment identifier is 3 Showing conservation header (""seq_conservation"" residue attribute) for alignment 3 Hiding conservation header for alignment 3 Chains used in RMSD evaluation for alignment 3: AlphaFold A0A1D7XF17_ALCSP #1/A, AlphaFold A8FEX8_BACP2 #4/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 3 RMSD between 309 pruned atom pairs is 0.468 angstroms; (across all 326 pairs: 1.749) > select #1/A:1-238,240-308,311-312 #4/A:2-239,241-309,312-313 4895 atoms, 5024 bonds, 618 residues, 2 models selected > select #1/A:290 #4/A:291 16 atoms, 14 bonds, 2 residues, 2 models selected > select #2/A:196 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:196-205 72 atoms, 72 bonds, 10 residues, 1 model selected > select #1/A:287 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:287-298 94 atoms, 95 bonds, 12 residues, 1 model selected > select #3/A:289 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:289-300 89 atoms, 89 bonds, 12 residues, 1 model selected > select #1/A:287 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:287-298 94 atoms, 95 bonds, 12 residues, 1 model selected > select #2/A:300 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:300-303 32 atoms, 31 bonds, 4 residues, 1 model selected > select #2/A:304 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:304-306 23 atoms, 22 bonds, 3 residues, 1 model selected Fetching A0A6I3IK90 UniProt info from https://www.uniprot.org/uniprot/A0A6I3IK90.xml > alphafold match A0A6I3IK90 1 UniProt id does not have an AlphaFold database model: A0A6I3IK90 (UniProt A0A6I3IK90) Fetching compressed AlphaFold A0A6I3IK90 from https://alphafold.ebi.ac.uk/files/AF-A0A6I3IK90-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A6I3IK90 (UniProt A0A6I3IK90) Opened 1 AlphaFold model > mmaker #5 to #1 showAlignment true 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold A0A6I3IK90_9MICO, chain A (#5), sequence alignment score = 815.5 Alignment identifier is 4 Showing conservation header (""seq_conservation"" residue attribute) for alignment 4 Hiding conservation header for alignment 4 Chains used in RMSD evaluation for alignment 4: AlphaFold A0A1D7XF17_ALCSP #1/A, AlphaFold A0A6I3IK90_9MICO #5/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 4 RMSD between 267 pruned atom pairs is 0.757 angstroms; (across all 326 pairs: 9.022) > mmaker #2 to #5 showAlignment true 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 AlphaFold A0A6I3IK90_9MICO, chain A (#5) with AlphaFold U7U7F7_9BURK, chain A (#2), sequence alignment score = 932.2 Alignment identifier is 5 Showing conservation header (""seq_conservation"" residue attribute) for alignment 5 Hiding conservation header for alignment 5 Chains used in RMSD evaluation for alignment 5: AlphaFold U7U7F7_9BURK #2/A, AlphaFold A0A6I3IK90_9MICO #5/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 5 RMSD between 290 pruned atom pairs is 0.708 angstroms; (across all 354 pairs: 13.030) > hide #1 models > hide #3 models > hide #4 models > hide #5 models > select clear > show #5 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #3 models > hide #3 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #1 models > hide #1 models > show #1 models > show #3 models > show #4 models > hide #4 models > hide #3 models > hide #1 models Fetching V4Y1C7 UniProt info from https://www.uniprot.org/uniprot/V4Y1C7.xml > alphafold match V4Y1C7 1 UniProt id does not have an AlphaFold database model: V4Y1C7 (UniProt V4Y1C7) Fetching compressed AlphaFold V4Y1C7 from https://alphafold.ebi.ac.uk/files/AF-V4Y1C7-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: V4Y1C7 (UniProt V4Y1C7) Opened 1 AlphaFold model > hide #5 models > show #5 models > mmaker #6 to #1 showAlignment true 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold V4Y1C7_9PROT, chain A (#6), sequence alignment score = 862.6 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: AlphaFold A0A1D7XF17_ALCSP #1/A, AlphaFold V4Y1C7_9PROT #6/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 272 pruned atom pairs is 0.789 angstroms; (across all 329 pairs: 8.216) > show #4 models > hide #4 models > hide #2 models > show #2 models > hide #2 models > hide #5 models > show #5 models > show #1 models > hide #1 models > show #3 models > hide #3 models > show #4 models Fetching A0A4Y9PQA1 UniProt info from https://www.uniprot.org/uniprot/A0A4Y9PQA1.xml > alphafold match A0A4Y9PQA1 1 UniProt id does not have an AlphaFold database model: A0A4Y9PQA1 (UniProt A0A4Y9PQA1) Fetching compressed AlphaFold A0A6D1IBG6 from https://alphafold.ebi.ac.uk/files/AF-A0A6D1IBG6-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A6D1IBG6 (UniProt A0A4Y9PQA1) Sequence Similarity --- AlphaFold Model| Query Sequence| Identity %| Coverage % A0A6D1IBG6_9MICO | A0A4Y9PQA1 | 100.0 | 100.0 Opened 1 AlphaFold model > mmaker #7 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold A0A6D1IBG6_9MICO, chain A (#7), sequence alignment score = 847.1 RMSD between 276 pruned atom pairs is 0.805 angstroms; (across all 327 pairs: 10.285) > show #1 models > hide #1 models > hide #5 models > hide #6 models > hide #7 models > show #7 models > show #6 models > show #5 models Fetching A0A1X3P4Z3 UniProt info from https://www.uniprot.org/uniprot/A0A1X3P4Z3.xml > alphafold match A0A1X3P4Z3 1 UniProt id does not have an AlphaFold database model: A0A1X3P4Z3 (UniProt A0A1X3P4Z3) Fetching compressed AlphaFold A0A1X3P4Z3 from https://alphafold.ebi.ac.uk/files/AF-A0A1X3P4Z3-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A1X3P4Z3 (UniProt A0A1X3P4Z3) Opened 1 AlphaFold model > mmaker #8 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold A0A1X3P4Z3_9MICC, chain A (#8), sequence alignment score = 842.2 RMSD between 279 pruned atom pairs is 0.781 angstroms; (across all 333 pairs: 8.300) Fetching A0A399JD64 UniProt info from https://www.uniprot.org/uniprot/A0A399JD64.xml > alphafold match A0A399JD64 1 UniProt id does not have an AlphaFold database model: A0A399JD64 (UniProt A0A399JD64) Fetching compressed AlphaFold A0A399JD64 from https://alphafold.ebi.ac.uk/files/AF-A0A399JD64-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A399JD64 (UniProt A0A399JD64) Opened 1 AlphaFold model > mmaker #9 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold A0A399JD64_9MICC, chain A (#9), sequence alignment score = 791.3 RMSD between 256 pruned atom pairs is 0.839 angstroms; (across all 333 pairs: 17.953) > hide #5 models > hide #6 models > hide #7 models > hide #8 models Fetching M0QIC5 UniProt info from https://www.uniprot.org/uniprot/M0QIC5.xml > alphafold match M0QIC5 1 UniProt id does not have an AlphaFold database model: M0QIC5 (UniProt M0QIC5) Fetching compressed AlphaFold M0QIC5 from https://alphafold.ebi.ac.uk/files/AF-M0QIC5-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: M0QIC5 (UniProt M0QIC5) Opened 1 AlphaFold model > hide #9 models > mmaker #10 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold M0QIC5_9ACTN, chain A (#10), sequence alignment score = 840.5 RMSD between 281 pruned atom pairs is 0.824 angstroms; (across all 332 pairs: 14.761) Fetching A0A0N1NB04 UniProt info from https://www.uniprot.org/uniprot/A0A0N1NB04.xml > alphafold match A0A0N1NB04 1 UniProt id does not have an AlphaFold database model: A0A0N1NB04 (UniProt A0A0N1NB04) Fetching compressed AlphaFold A0A0N1NB04 from https://alphafold.ebi.ac.uk/files/AF-A0A0N1NB04-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A0N1NB04 (UniProt A0A0N1NB04) Opened 1 AlphaFold model > mmaker #11 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold A0A0N1NB04_9ACTN, chain A (#11), sequence alignment score = 791 RMSD between 278 pruned atom pairs is 0.785 angstroms; (across all 329 pairs: 7.826) > hide #10 models Fetching A0A3A4KI50 UniProt info from https://www.uniprot.org/uniprot/A0A3A4KI50.xml > alphafold match A0A3A4KI50 1 UniProt id does not have an AlphaFold database model: A0A3A4KI50 (UniProt A0A3A4KI50) Fetching compressed AlphaFold A0A3A4KI50 from https://alphafold.ebi.ac.uk/files/AF-A0A3A4KI50-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A3A4KI50 (UniProt A0A3A4KI50) Opened 1 AlphaFold model > mmaker #12 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold A0A3A4KI50_9NOCA, chain A (#12), sequence alignment score = 813.4 RMSD between 272 pruned atom pairs is 0.781 angstroms; (across all 319 pairs: 8.900) > hide #11 models Fetching A0A6G4V0U3 UniProt info from https://www.uniprot.org/uniprot/A0A6G4V0U3.xml > alphafold match A0A6G4V0U3 1 UniProt id does not have an AlphaFold database model: A0A6G4V0U3 (UniProt A0A6G4V0U3) Fetching compressed AlphaFold A0A6G4V0U3 from https://alphafold.ebi.ac.uk/files/AF-A0A6G4V0U3-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A6G4V0U3 (UniProt A0A6G4V0U3) Opened 1 AlphaFold model > mmaker #13 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 AlphaFold A0A1D7XF17_ALCSP, chain A (#1) with AlphaFold A0A6G4V0U3_9ACTN, chain A (#13), sequence alignment score = 875.3 RMSD between 272 pruned atom pairs is 0.711 angstroms; (across all 325 pairs: 5.931) > hide #12 models > close #1 > close #2 > close #3 > hide #4 models > hide #13 models > open ""I:/Mi > unidad/Santiago/BIO_INF_TEC_URP/Bacillus/Resultados/Cryo_EM/QHYN/pdb_analysis_sessions/CynD_chainA.pdb"" Chain information for CynD_chainA.pdb #1 --- Chain | Description A | No description available > mmaker #1 to #4 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 AlphaFold A8FEX8_BACP2, chain A (#4) with CynD_chainA.pdb, chain A (#1), sequence alignment score = 1595.4 RMSD between 295 pruned atom pairs is 0.684 angstroms; (across all 315 pairs: 1.961) > show #4 models > mmaker #1 to #4 showAlignment true 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 AlphaFold A8FEX8_BACP2, chain A (#4) with CynD_chainA.pdb, chain A (#1), sequence alignment score = 1595.4 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: CynD_chainA.pdb #1/A, AlphaFold A8FEX8_BACP2 #4/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 295 pruned atom pairs is 0.684 angstroms; (across all 315 pairs: 1.961) > select #4/A:321 12 atoms, 12 bonds, 1 residue, 1 model selected > select #4/A:321-330 84 atoms, 84 bonds, 10 residues, 1 model selected > hide #4 models > show #4 models > hide #4 models > mmaker #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 CynD_chainA.pdb, chain A (#1) with AlphaFold A8FEX8_BACP2, chain A (#4), sequence alignment score = 1595.4 RMSD between 295 pruned atom pairs is 0.684 angstroms; (across all 315 pairs: 1.961) > mmaker #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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A6I3IK90_9MICO, chain A (#5), sequence alignment score = 757.8 RMSD between 247 pruned atom pairs is 0.876 angstroms; (across all 314 pairs: 9.178) > mmaker #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 CynD_chainA.pdb, chain A (#1) with AlphaFold V4Y1C7_9PROT, chain A (#6), sequence alignment score = 816.2 RMSD between 256 pruned atom pairs is 0.876 angstroms; (across all 314 pairs: 3.929) > mmaker #7 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A6D1IBG6_9MICO, chain A (#7), sequence alignment score = 784.9 RMSD between 264 pruned atom pairs is 0.895 angstroms; (across all 312 pairs: 6.515) > mmaker #8 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A1X3P4Z3_9MICC, chain A (#8), sequence alignment score = 806.5 RMSD between 258 pruned atom pairs is 0.951 angstroms; (across all 310 pairs: 3.320) > mmaker #9 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A399JD64_9MICC, chain A (#9), sequence alignment score = 741.7 RMSD between 245 pruned atom pairs is 0.944 angstroms; (across all 310 pairs: 7.132) > mmaker #10 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 CynD_chainA.pdb, chain A (#1) with AlphaFold M0QIC5_9ACTN, chain A (#10), sequence alignment score = 763.9 RMSD between 257 pruned atom pairs is 0.904 angstroms; (across all 314 pairs: 8.327) > mmaker #11 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A0N1NB04_9ACTN, chain A (#11), sequence alignment score = 738.5 RMSD between 271 pruned atom pairs is 0.909 angstroms; (across all 314 pairs: 3.426) > mmaker #12 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A3A4KI50_9NOCA, chain A (#12), sequence alignment score = 759.5 RMSD between 264 pruned atom pairs is 0.972 angstroms; (across all 309 pairs: 5.336) > mmaker #13 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A6G4V0U3_9ACTN, chain A (#13), sequence alignment score = 801.2 RMSD between 270 pruned atom pairs is 0.856 angstroms; (across all 310 pairs: 3.292) > show #5 models > show #6 models > show #7 models > show #8 models > show #9 models > show #10 models > show #11 models > show #12 models > show #13 models > show #4 models > hide #4 models > mmaker #5 to #1 showAlignment true 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A6I3IK90_9MICO, chain A (#5), sequence alignment score = 757.8 Alignment identifier is 2 Showing conservation header (""seq_conservation"" residue attribute) for alignment 2 Hiding conservation header for alignment 2 Chains used in RMSD evaluation for alignment 2: CynD_chainA.pdb #1/A, AlphaFold A0A6I3IK90_9MICO #5/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2 RMSD between 247 pruned atom pairs is 0.876 angstroms; (across all 314 pairs: 9.178) > select #5/A:61 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:61-69 58 atoms, 57 bonds, 9 residues, 1 model selected > hide #5 models > hide #6 models > hide #7 models > hide #8 models > hide #9 models > hide #10 models > hide #12 models > hide #11 models > hide #13 models > show #5 models > select #5/A:109 4 atoms, 3 bonds, 1 residue, 1 model selected > select #5/A:109-110 9 atoms, 8 bonds, 2 residues, 1 model selected > select #5/A:192 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:192-207 129 atoms, 132 bonds, 16 residues, 1 model selected > select #1/A:232 24 atoms, 23 bonds, 1 residue, 1 model selected > select #1/A:232-239 148 atoms, 150 bonds, 8 residues, 1 model selected > show #6 models > show #7 models > show #8 models > show #4 models > hide #5 models > hide #6 models > hide #7 models > hide #8 models > show #5 models > show #6 models > hide #6 models > hide #4 models > hide #5 models > select #5/A:300 11 atoms, 10 bonds, 1 residue, 1 model selected > select #5/A:300-314 119 atoms, 121 bonds, 15 residues, 1 model selected > show #5 models > hide #5 models > hide #1 models > show #1 models > hide #1 models > save ""I:/Mi > unidad/Santiago/BIO_INF_TEC_URP/Bacillus/Resultados/Bioinf/Tesis_David/id_char_muts/par2_vs_CynD.cxs"" ——— End of log from Sun Apr 30 01:02:17 2023 ——— opened ChimeraX session > rainbow structures > select add #5 2878 atoms, 2949 bonds, 378 residues, 1 model selected > select subtract #5 Nothing selected > select add #5 2878 atoms, 2949 bonds, 378 residues, 1 model selected > select subtract #5 Nothing selected > show #1 models > show #4 models > hide #4 models > show #5 models > show #6 models > hide #5 models > hide #6 models > show #7 models > hide #7 models > show #8 models > hide #8 models > show #9 models > hide #9 models > show #10 models > hide #10 models > show #11 models > hide #11 models > show #12 models > hide #12 models > show #13 models > hide #13 models > ui tool show Shell QWindowsWindow::setGeometry: Unable to set geometry 579x370+2009+834 (frame: 601x426+1998+789) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 573x353+2012+848 (frame: 595x409+2001+803) margins: 11, 45, 11, 11 minimum size: 78x1 maximum size: 524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=139, y=58))) > ui tool show AlphaFold Fetching A0A0J8YTP9 UniProt info from https://www.uniprot.org/uniprot/A0A0J8YTP9.xml > alphafold match A0A0J8YTP9 1 UniProt id does not have an AlphaFold database model: A0A0J8YTP9 (UniProt A0A0J8YTP9) Fetching compressed AlphaFold A0A0J8YTP9 from https://alphafold.ebi.ac.uk/files/AF-A0A0J8YTP9-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A0J8YTP9 (UniProt A0A0J8YTP9) Opened 1 AlphaFold model > alphafold match A0A0J8YTP9 1 UniProt id does not have an AlphaFold database model: A0A0J8YTP9 (UniProt A0A0J8YTP9) 1 AlphaFold model found using sequence similarity searches: A0A0J8YTP9 (UniProt A0A0J8YTP9) Opened 1 AlphaFold model > select down Nothing selected > select down Nothing selected > select down Nothing selected > select down Nothing selected > close 2 Expected a models specifier or a keyword > close #2 > close #3 > close #4 > close #5 > close #6 > close #7 > close #8 > close #9 > close #10 > close #11 > close #12 > close #13 Fetching A0A0J8YTP9 UniProt info from https://www.uniprot.org/uniprot/A0A0J8YTP9.xml > alphafold match A0A0J8YTP9 1 UniProt id does not have an AlphaFold database model: A0A0J8YTP9 (UniProt A0A0J8YTP9) Fetching compressed AlphaFold A0A0J8YTP9 from https://alphafold.ebi.ac.uk/files/AF-A0A0J8YTP9-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A0J8YTP9 (UniProt A0A0J8YTP9) Opened 1 AlphaFold model Fetching D2TWZ9 UniProt info from https://www.uniprot.org/uniprot/D2TWZ9.xml > alphafold match D2TWZ9 1 UniProt id does not have an AlphaFold database model: D2TWZ9 (UniProt D2TWZ9) Fetching compressed AlphaFold D2TWZ9 from https://alphafold.ebi.ac.uk/files/AF-D2TWZ9-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: D2TWZ9 (UniProt D2TWZ9) Opened 1 AlphaFold model Fetching V2TN35 UniProt info from https://www.uniprot.org/uniprot/V2TN35.xml > alphafold match V2TN35 1 UniProt id does not have an AlphaFold database model: V2TN35 (UniProt V2TN35) Fetching compressed AlphaFold V2TN35 from https://alphafold.ebi.ac.uk/files/AF-V2TN35-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: V2TN35 (UniProt V2TN35) Opened 1 AlphaFold model Fetching B8KVK8 UniProt info from https://www.uniprot.org/uniprot/B8KVK8.xml > alphafold match B8KVK8 1 UniProt id does not have an AlphaFold database model: B8KVK8 (UniProt B8KVK8) Fetching compressed AlphaFold B8KVK8 from https://alphafold.ebi.ac.uk/files/AF-B8KVK8-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: B8KVK8 (UniProt B8KVK8) Opened 1 AlphaFold model Fetching B1KMA0 UniProt info from https://www.uniprot.org/uniprot/B1KMA0.xml > alphafold match B1KMA0 1 UniProt id does not have an AlphaFold database model: B1KMA0 (UniProt B1KMA0) Fetching compressed AlphaFold B1KMA0 from https://alphafold.ebi.ac.uk/files/AF-B1KMA0-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: B1KMA0 (UniProt B1KMA0) Opened 1 AlphaFold model Fetching A0A4V2ZFV7 UniProt info from https://www.uniprot.org/uniprot/A0A4V2ZFV7.xml > alphafold match A0A4V2ZFV7 1 UniProt id does not have an AlphaFold database model: A0A4V2ZFV7 (UniProt A0A4V2ZFV7) Fetching compressed AlphaFold A0A4V2ZFV7 from https://alphafold.ebi.ac.uk/files/AF-A0A4V2ZFV7-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A4V2ZFV7 (UniProt A0A4V2ZFV7) Opened 1 AlphaFold model Fetching A0A5S3PMU3 UniProt info from https://www.uniprot.org/uniprot/A0A5S3PMU3.xml > alphafold match A0A5S3PMU3 1 UniProt id does not have an AlphaFold database model: A0A5S3PMU3 (UniProt A0A5S3PMU3) Fetching compressed AlphaFold A0A5S3PMU3 from https://alphafold.ebi.ac.uk/files/AF-A0A5S3PMU3-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A5S3PMU3 (UniProt A0A5S3PMU3) Opened 1 AlphaFold model Fetching A5V4Y8 UniProt info from https://www.uniprot.org/uniprot/A5V4Y8.xml > alphafold match A5V4Y8 Fetching A0A3A1P588 UniProt info from https://www.uniprot.org/uniprot/A0A3A1P588.xml > alphafold match A0A3A1P588 1 UniProt id does not have an AlphaFold database model: A0A3A1P588 (UniProt A0A3A1P588) Fetching compressed AlphaFold A0A3A1P588 from https://alphafold.ebi.ac.uk/files/AF-A0A3A1P588-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A3A1P588 (UniProt A0A3A1P588) Opened 1 AlphaFold model Fetching F6IEF9 UniProt info from https://www.uniprot.org/uniprot/F6IEF9.xml > alphafold match F6IEF9 1 UniProt id does not have an AlphaFold database model: F6IEF9 (UniProt F6IEF9) Fetching compressed AlphaFold F6IEF9 from https://alphafold.ebi.ac.uk/files/AF-F6IEF9-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: F6IEF9 (UniProt F6IEF9) Opened 1 AlphaFold model Fetching A0A480AHR2 UniProt info from https://www.uniprot.org/uniprot/A0A480AHR2.xml > alphafold match A0A480AHR2 1 UniProt id does not have an AlphaFold database model: A0A480AHR2 (UniProt A0A480AHR2) Fetching compressed AlphaFold A0A480AHR2 from https://alphafold.ebi.ac.uk/files/AF-A0A480AHR2-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A480AHR2 (UniProt A0A480AHR2) Opened 1 AlphaFold model Fetching A0A4R7PEM6 UniProt info from https://www.uniprot.org/uniprot/A0A4R7PEM6.xml > alphafold match A0A4R7PEM6 1 UniProt id does not have an AlphaFold database model: A0A4R7PEM6 (UniProt A0A4R7PEM6) Fetching compressed AlphaFold A0A4R7PEM6 from https://alphafold.ebi.ac.uk/files/AF-A0A4R7PEM6-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A4R7PEM6 (UniProt A0A4R7PEM6) Opened 1 AlphaFold model Fetching L1M139 UniProt info from https://www.uniprot.org/uniprot/L1M139.xml > alphafold match L1M139 1 UniProt id does not have an AlphaFold database model: L1M139 (UniProt L1M139) Fetching compressed AlphaFold L1M139 from https://alphafold.ebi.ac.uk/files/AF-L1M139-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: L1M139 (UniProt L1M139) Opened 1 AlphaFold model Fetching A0A4Q8URY2 UniProt info from https://www.uniprot.org/uniprot/A0A4Q8URY2.xml > alphafold match A0A4Q8URY2 1 UniProt id does not have an AlphaFold database model: A0A4Q8URY2 (UniProt A0A4Q8URY2) Fetching compressed AlphaFold A0A4Q8URY2 from https://alphafold.ebi.ac.uk/files/AF-A0A4Q8URY2-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A4Q8URY2 (UniProt A0A4Q8URY2) Opened 1 AlphaFold model Fetching A9D6L7 UniProt info from https://www.uniprot.org/uniprot/A9D6L7.xml > alphafold match A9D6L7 1 UniProt id does not have an AlphaFold database model: A9D6L7 (UniProt A9D6L7) Fetching compressed AlphaFold A9D6L7 from https://alphafold.ebi.ac.uk/files/AF-A9D6L7-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A9D6L7 (UniProt A9D6L7) Opened 1 AlphaFold model Fetching I4CEN7 UniProt info from https://www.uniprot.org/uniprot/I4CEN7.xml > alphafold match I4CEN7 1 UniProt id does not have an AlphaFold database model: I4CEN7 (UniProt I4CEN7) Fetching compressed AlphaFold I4CEN7 from https://alphafold.ebi.ac.uk/files/AF-I4CEN7-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: I4CEN7 (UniProt I4CEN7) Opened 1 AlphaFold model Fetching A0A370N3U6 UniProt info from https://www.uniprot.org/uniprot/A0A370N3U6.xml > alphafold match A0A370N3U6 1 UniProt id does not have an AlphaFold database model: A0A370N3U6 (UniProt A0A370N3U6) Fetching compressed AlphaFold A0A370N3U6 from https://alphafold.ebi.ac.uk/files/AF-A0A370N3U6-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A370N3U6 (UniProt A0A370N3U6) Opened 1 AlphaFold model Fetching A0A1L9B491 UniProt info from https://www.uniprot.org/uniprot/A0A1L9B491.xml > alphafold match A0A1L9B491 1 UniProt id does not have an AlphaFold database model: A0A1L9B491 (UniProt A0A1L9B491) Fetching compressed AlphaFold A0A1L9B491 from https://alphafold.ebi.ac.uk/files/AF-A0A1L9B491-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A1L9B491 (UniProt A0A1L9B491) Opened 1 AlphaFold model Fetching A0A1H0LGU0 UniProt info from https://www.uniprot.org/uniprot/A0A1H0LGU0.xml > alphafold match A0A1H0LGU0 1 UniProt id does not have an AlphaFold database model: A0A1H0LGU0 (UniProt A0A1H0LGU0) Fetching compressed AlphaFold A0A1H0LGU0 from https://alphafold.ebi.ac.uk/files/AF-A0A1H0LGU0-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A1H0LGU0 (UniProt A0A1H0LGU0) Opened 1 AlphaFold model Fetching A0A1G5QFQ9 UniProt info from https://www.uniprot.org/uniprot/A0A1G5QFQ9.xml > alphafold match A0A1G5QFQ9 1 UniProt id does not have an AlphaFold database model: A0A1G5QFQ9 (UniProt A0A1G5QFQ9) Fetching compressed AlphaFold A0A1G5QFQ9 from https://alphafold.ebi.ac.uk/files/AF-A0A1G5QFQ9-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A1G5QFQ9 (UniProt A0A1G5QFQ9) Opened 1 AlphaFold model Fetching A0A4Q1KIU1 UniProt info from https://www.uniprot.org/uniprot/A0A4Q1KIU1.xml > alphafold match A0A4Q1KIU1 1 UniProt id does not have an AlphaFold database model: A0A4Q1KIU1 (UniProt A0A4Q1KIU1) Fetching compressed AlphaFold A0A4Q1KIU1 from https://alphafold.ebi.ac.uk/files/AF-A0A4Q1KIU1-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A4Q1KIU1 (UniProt A0A4Q1KIU1) Opened 1 AlphaFold model Fetching A0A0N0VI24 UniProt info from https://www.uniprot.org/uniprot/A0A0N0VI24.xml > alphafold match A0A0N0VI24 1 UniProt id does not have an AlphaFold database model: A0A0N0VI24 (UniProt A0A0N0VI24) Fetching compressed AlphaFold A0A0N0VI24 from https://alphafold.ebi.ac.uk/files/AF-A0A0N0VI24-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A0N0VI24 (UniProt A0A0N0VI24) Opened 1 AlphaFold model Fetching A0A060QHL9 UniProt info from https://www.uniprot.org/uniprot/A0A060QHL9.xml > alphafold match A0A060QHL9 1 UniProt id does not have an AlphaFold database model: A0A060QHL9 (UniProt A0A060QHL9) Fetching compressed AlphaFold A0A060QHL9 from https://alphafold.ebi.ac.uk/files/AF-A0A060QHL9-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A060QHL9 (UniProt A0A060QHL9) Opened 1 AlphaFold model Fetching A0A1N6UIB7 UniProt info from https://www.uniprot.org/uniprot/A0A1N6UIB7.xml > alphafold match A0A1N6UIB7 1 UniProt id does not have an AlphaFold database model: A0A1N6UIB7 (UniProt A0A1N6UIB7) Fetching compressed AlphaFold A0A1N6UIB7 from https://alphafold.ebi.ac.uk/files/AF-A0A1N6UIB7-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A1N6UIB7 (UniProt A0A1N6UIB7) Opened 1 AlphaFold model Fetching A0A1I4SMV6 UniProt info from https://www.uniprot.org/uniprot/A0A1I4SMV6.xml > alphafold match A0A1I4SMV6 1 UniProt id does not have an AlphaFold database model: A0A1I4SMV6 (UniProt A0A1I4SMV6) Fetching compressed AlphaFold A0A1I4SMV6 from https://alphafold.ebi.ac.uk/files/AF-A0A1I4SMV6-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A1I4SMV6 (UniProt A0A1I4SMV6) Opened 1 AlphaFold model Fetching A0A1I5SZE4 UniProt info from https://www.uniprot.org/uniprot/A0A1I5SZE4.xml > alphafold match A0A1I5SZE4 1 UniProt id does not have an AlphaFold database model: A0A1I5SZE4 (UniProt A0A1I5SZE4) Fetching compressed AlphaFold A0A1I5SZE4 from https://alphafold.ebi.ac.uk/files/AF-A0A1I5SZE4-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A1I5SZE4 (UniProt A0A1I5SZE4) Opened 1 AlphaFold model Fetching A0P008 UniProt info from https://www.uniprot.org/uniprot/A0P008.xml > alphafold match A0P008 1 UniProt id does not have an AlphaFold database model: A0P008 (UniProt A0P008) Fetching compressed AlphaFold A0P008 from https://alphafold.ebi.ac.uk/files/AF-A0P008-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0P008 (UniProt A0P008) Opened 1 AlphaFold model Fetching A0A2R4MHN4 UniProt info from https://www.uniprot.org/uniprot/A0A2R4MHN4.xml > alphafold match A0A2R4MHN4 1 UniProt id does not have an AlphaFold database model: A0A2R4MHN4 (UniProt A0A2R4MHN4) Fetching compressed AlphaFold A0A2R4MHN4 from https://alphafold.ebi.ac.uk/files/AF-A0A2R4MHN4-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A2R4MHN4 (UniProt A0A2R4MHN4) Opened 1 AlphaFold model Fetching Q28KW0 UniProt info from https://www.uniprot.org/uniprot/Q28KW0.xml > alphafold match Q28KW0 1 UniProt id does not have an AlphaFold database model: Q28KW0 (UniProt Q28KW0) Fetching compressed AlphaFold Q28KW0 from https://alphafold.ebi.ac.uk/files/AF-Q28KW0-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: Q28KW0 (UniProt Q28KW0) Opened 1 AlphaFold model Fetching A0A1H4HM05 UniProt info from https://www.uniprot.org/uniprot/A0A1H4HM05.xml > alphafold match A0A1H4HM05 1 UniProt id does not have an AlphaFold database model: A0A1H4HM05 (UniProt A0A1H4HM05) Fetching compressed AlphaFold A0A1H4HM05 from https://alphafold.ebi.ac.uk/files/AF-A0A1H4HM05-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A1H4HM05 (UniProt A0A1H4HM05) Opened 1 AlphaFold model Fetching A0A2Z2NN35 UniProt info from https://www.uniprot.org/uniprot/A0A2Z2NN35.xml > alphafold match A0A2Z2NN35 1 UniProt id does not have an AlphaFold database model: A0A2Z2NN35 (UniProt A0A2Z2NN35) Fetching compressed AlphaFold A0A2Z2NN35 from https://alphafold.ebi.ac.uk/files/AF-A0A2Z2NN35-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A2Z2NN35 (UniProt A0A2Z2NN35) Opened 1 AlphaFold model Fetching U7U7F7 UniProt info from https://www.uniprot.org/uniprot/U7U7F7.xml > alphafold match U7U7F7 1 UniProt id does not have an AlphaFold database model: U7U7F7 (UniProt U7U7F7) Fetching compressed AlphaFold U7U7F7 from https://alphafold.ebi.ac.uk/files/AF-U7U7F7-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: U7U7F7 (UniProt U7U7F7) Opened 1 AlphaFold model > mmaker #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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A0J8YTP9_9GAMM, chain A (#2), sequence alignment score = 758.8 RMSD between 244 pruned atom pairs is 0.895 angstroms; (across all 309 pairs: 6.331) > mmaker #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 CynD_chainA.pdb, chain A (#1) with AlphaFold D2TWZ9_9GAMM, chain A (#3), sequence alignment score = 764.3 RMSD between 244 pruned atom pairs is 0.881 angstroms; (across all 312 pairs: 9.634) > mmaker #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 CynD_chainA.pdb, chain A (#1) with AlphaFold V2TN35_9GAMM, chain A (#4), sequence alignment score = 805.5 RMSD between 260 pruned atom pairs is 0.918 angstroms; (across all 305 pairs: 5.915) > mmaker #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 CynD_chainA.pdb, chain A (#1) with AlphaFold B8KVK8_9GAMM, chain A (#5), sequence alignment score = 819.3 RMSD between 258 pruned atom pairs is 0.874 angstroms; (across all 313 pairs: 8.557) > mmaker #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 CynD_chainA.pdb, chain A (#1) with AlphaFold B1KMA0_SHEWM, chain A (#6), sequence alignment score = 810.8 RMSD between 261 pruned atom pairs is 0.915 angstroms; (across all 313 pairs: 7.161) > mmaker #7 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A4V2ZFV7_9ALTE, chain A (#7), sequence alignment score = 824.8 RMSD between 270 pruned atom pairs is 0.883 angstroms; (across all 314 pairs: 6.307) > mmaker #8 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A5S3PMU3_9FLAO, chain A (#8), sequence alignment score = 808.4 RMSD between 259 pruned atom pairs is 0.924 angstroms; (across all 311 pairs: 11.357) > mmaker #9 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A3A1P588_9SPHN, chain A (#9), sequence alignment score = 798.1 RMSD between 254 pruned atom pairs is 0.891 angstroms; (across all 311 pairs: 5.373) > mmaker #10 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 CynD_chainA.pdb, chain A (#1) with AlphaFold F6IEF9_9SPHN, chain A (#10), sequence alignment score = 545.8 RMSD between 194 pruned atom pairs is 0.944 angstroms; (across all 243 pairs: 7.281) > mmaker #11 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A480AHR2_9BURK, chain A (#11), sequence alignment score = 809.6 RMSD between 255 pruned atom pairs is 0.872 angstroms; (across all 312 pairs: 6.300) > mmaker #12 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A4R7PEM6_9GAMM, chain A (#12), sequence alignment score = 773 RMSD between 255 pruned atom pairs is 0.859 angstroms; (across all 314 pairs: 9.132) > mmaker #13 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 CynD_chainA.pdb, chain A (#1) with AlphaFold L1M139_PSEPU, chain A (#13), sequence alignment score = 819.7 RMSD between 259 pruned atom pairs is 0.880 angstroms; (across all 314 pairs: 11.981) > mmaker #14 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A4Q8URY2_9MICC, chain A (#14), sequence alignment score = 827.9 RMSD between 249 pruned atom pairs is 0.899 angstroms; (across all 308 pairs: 6.811) > mmaker #15 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A9D6L7_HOEPD, chain A (#15), sequence alignment score = 828 RMSD between 261 pruned atom pairs is 0.894 angstroms; (across all 309 pairs: 6.317) > mmaker #16 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 CynD_chainA.pdb, chain A (#1) with AlphaFold I4CEN7_DESTA, chain A (#16), sequence alignment score = 861.5 RMSD between 263 pruned atom pairs is 0.858 angstroms; (across all 309 pairs: 8.262) > mmaker #17 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A370N3U6_9BURK, chain A (#17), sequence alignment score = 776.1 RMSD between 252 pruned atom pairs is 0.881 angstroms; (across all 310 pairs: 6.668) > mmaker #18 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A1L9B491_9DELT, chain A (#18), sequence alignment score = 803.5 RMSD between 258 pruned atom pairs is 0.827 angstroms; (across all 310 pairs: 8.245) > mmaker #19 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A1H0LGU0_9BRAD, chain A (#19), sequence alignment score = 767.2 RMSD between 245 pruned atom pairs is 0.827 angstroms; (across all 304 pairs: 6.407) > mmaker #20 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A1G5QFQ9_9RHOB, chain A (#20), sequence alignment score = 812.5 RMSD between 248 pruned atom pairs is 0.841 angstroms; (across all 305 pairs: 7.987) > mmaker #21 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A4Q1KIU1_9SPHN, chain A (#21), sequence alignment score = 803.3 RMSD between 266 pruned atom pairs is 0.927 angstroms; (across all 309 pairs: 3.649) > mmaker #22 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A0N0VI24_9PSED, chain A (#22), sequence alignment score = 813 RMSD between 258 pruned atom pairs is 0.854 angstroms; (across all 314 pairs: 11.371) > mmaker #23 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A060QHL9_9PROT, chain A (#23), sequence alignment score = 762.8 RMSD between 256 pruned atom pairs is 0.919 angstroms; (across all 307 pairs: 6.450) > mmaker #24 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A1N6UIB7_9GAMM, chain A (#24), sequence alignment score = 822.9 RMSD between 266 pruned atom pairs is 0.892 angstroms; (across all 314 pairs: 11.556) > mmaker #25 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A1I4SMV6_9RHOB, chain A (#25), sequence alignment score = 769.3 RMSD between 246 pruned atom pairs is 0.824 angstroms; (across all 295 pairs: 4.488) > mmaker #26 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A1I5SZE4_9BURK, chain A (#26), sequence alignment score = 735.4 RMSD between 260 pruned atom pairs is 0.908 angstroms; (across all 305 pairs: 4.645) > mmaker #27 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0P008_LABAI, chain A (#27), sequence alignment score = 803.6 RMSD between 257 pruned atom pairs is 0.890 angstroms; (across all 313 pairs: 2.941) > mmaker #28 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A2R4MHN4_9HYPH, chain A (#28), sequence alignment score = 790.9 RMSD between 264 pruned atom pairs is 0.908 angstroms; (across all 314 pairs: 6.709) > mmaker #29 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 CynD_chainA.pdb, chain A (#1) with AlphaFold Q28KW0_JANSC, chain A (#29), sequence alignment score = 806.6 RMSD between 248 pruned atom pairs is 0.888 angstroms; (across all 311 pairs: 8.054) > mmaker #30 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A1H4HM05_9BURK, chain A (#30), sequence alignment score = 800.8 RMSD between 262 pruned atom pairs is 0.935 angstroms; (across all 309 pairs: 3.307) > mmaker #31 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 CynD_chainA.pdb, chain A (#1) with AlphaFold A0A2Z2NN35_9GAMM, chain A (#31), sequence alignment score = 774.6 RMSD between 253 pruned atom pairs is 0.896 angstroms; (across all 305 pairs: 6.732) > mmaker #32 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 CynD_chainA.pdb, chain A (#1) with AlphaFold U7U7F7_9BURK, chain A (#32), sequence alignment score = 726.3 RMSD between 256 pruned atom pairs is 0.900 angstroms; (across all 313 pairs: 9.758) > rainbow structures > hide ~#1 ribbons > show #2 ribbons > hide #2 models > show #3 ribbons > hide #3 models > show #4 ribbons > hide #4 models > show #5 ribbons > hide #5 models > show #5 ribbons > show #6 ribbons > show #2 models > hide #2 models > show #2 models > show #3 models > hide #3 models > show #3 models > show #4 models > hide #4 models > show #4 models > hide #3 models > hide #4 models > hide #2 models > hide #6 models > show #7 ribbons > hide #7 models > show #8 ribbons > hide #8 models > show #9 ribbons > hide #9 models > show #10 ribbons > hide #10 models > show #11 ribbons > hide #11 models > show #12 ribbons > hide #12 models > show #13 ribbons > hide #13 models > show #14 ribbons > hide #14 models > show #15 ribbons > show #15 atoms,ribbons > hide #15 atoms,ribbons > alphafold pae #15 uniprotId A9D6L7 Fetching compressed AlphaFold PAE A9D6L7 from https://alphafold.ebi.ac.uk/files/AF-A9D6L7-F1-predicted_aligned_error_v4.json > hide #15 models > show #16 ribbons > hide #16 models > show #17 ribbons > show #18 ribbons > hide #17 models > show #19 ribbons > hide #18 models > show #20 ribbons > show #21 ribbons > show #22 ribbons > show #23 ribbons > show #24 ribbons > show #25 ribbons > hide #19 models > hide #20 models > hide #21 models > hide #22 models > hide #23 models > hide #24 models > show #26 ribbons > show #27 ribbons > show #278 ribbons > show #28 ribbons > show #29 ribbons > show #30 ribbons > show #31 ribbons > hide #25 models > hide #26 models > hide #27 models > hide #28 models > hide #29 models > hide #30 models > show #32 ribbons > hide #31 models > hide #32 models > save ""I:/Mi > unidad/Santiago/BIO_INF_TEC_URP/Bacillus/Resultados/Bioinf/Tesis_David/id_char_muts/par1_vs_CynD.cxs"" ——— End of log from Sun Apr 30 21:29:43 2023 ——— opened ChimeraX session QWindowsWindow::setGeometry: Unable to set geometry 581x149+2010+1205 (frame: 603x205+1999+1160) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 575x132+2013+1219 (frame: 597x188+2002+1174) margins: 11, 45, 11, 11 minimum size: 142x72 maximum size: 524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=235, y=164))) > show #2 models > ui tool show ""Ramachandran Plot"" Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\matplotlib\cbook\\__init__.py"", line 287, in process func(*args, **kwargs) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\validation\ramaplot\ramaplot.py"", line 307, in on_pick get_stepper(self.current_model).step_to(picked_rama.residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 143, in step_to self._new_camera_position(residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 232, in _new_camera_position interpolate_camera(session, 0, frames=1) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 217, in interpolate_camera ncp, fcp = _get_clip_points(session, dist) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 360, in _get_clip_points return (o+vd*dist*0.5, o+vd*dist*1.5) UnboundLocalError: local variable 'o' referenced before assignment Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\matplotlib\cbook\\__init__.py"", line 287, in process func(*args, **kwargs) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\validation\ramaplot\ramaplot.py"", line 307, in on_pick get_stepper(self.current_model).step_to(picked_rama.residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 143, in step_to self._new_camera_position(residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 232, in _new_camera_position interpolate_camera(session, 0, frames=1) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 217, in interpolate_camera ncp, fcp = _get_clip_points(session, dist) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 360, in _get_clip_points return (o+vd*dist*0.5, o+vd*dist*1.5) UnboundLocalError: local variable 'o' referenced before assignment Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\matplotlib\cbook\\__init__.py"", line 287, in process func(*args, **kwargs) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\validation\ramaplot\ramaplot.py"", line 307, in on_pick get_stepper(self.current_model).step_to(picked_rama.residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 143, in step_to self._new_camera_position(residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 232, in _new_camera_position interpolate_camera(session, 0, frames=1) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 217, in interpolate_camera ncp, fcp = _get_clip_points(session, dist) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 360, in _get_clip_points return (o+vd*dist*0.5, o+vd*dist*1.5) UnboundLocalError: local variable 'o' referenced before assignment > hide #2 models > ui tool show ""Ramachandran Plot"" > show #!2 models > hide #!2 models > hide #1 models > show #1 models > show ribbons > select add #1 4908 atoms, 4976 bonds, 315 residues, 1 model selected > select subtract #1 Nothing selected > select add #1 4908 atoms, 4976 bonds, 315 residues, 1 model selected > view sel > hide #1 models > show #1 models > show #!2 models > select clear > show #3 models > hide #!2 models > show #4 models > hide #3 models > show #5 models > hide #4 models > show #4 models > hide #4 models > hide #5 models > ui tool show ""Ramachandran Plot"" > select #1/A:36 15 atoms, 14 bonds, 1 residue, 1 model selected > select up 223 atoms, 222 bonds, 15 residues, 1 model selected > select clear > select #1/A:200 24 atoms, 23 bonds, 1 residue, 1 model selected > select up 175 atoms, 176 bonds, 11 residues, 1 model selected > select clear > select #1/A:104 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 149 atoms, 149 bonds, 10 residues, 1 model selected Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\matplotlib\cbook\\__init__.py"", line 287, in process func(*args, **kwargs) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\validation\ramaplot\ramaplot.py"", line 307, in on_pick get_stepper(self.current_model).step_to(picked_rama.residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 143, in step_to self._new_camera_position(residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 232, in _new_camera_position interpolate_camera(session, 0, frames=1) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 217, in interpolate_camera ncp, fcp = _get_clip_points(session, dist) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 360, in _get_clip_points return (o+vd*dist*0.5, o+vd*dist*1.5) UnboundLocalError: local variable 'o' referenced before assignment Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\matplotlib\cbook\\__init__.py"", line 287, in process func(*args, **kwargs) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\validation\ramaplot\ramaplot.py"", line 307, in on_pick get_stepper(self.current_model).step_to(picked_rama.residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 143, in step_to self._new_camera_position(residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 232, in _new_camera_position interpolate_camera(session, 0, frames=1) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 217, in interpolate_camera ncp, fcp = _get_clip_points(session, dist) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 360, in _get_clip_points return (o+vd*dist*0.5, o+vd*dist*1.5) UnboundLocalError: local variable 'o' referenced before assignment Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\matplotlib\cbook\\__init__.py"", line 287, in process func(*args, **kwargs) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\validation\ramaplot\ramaplot.py"", line 307, in on_pick get_stepper(self.current_model).step_to(picked_rama.residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 143, in step_to self._new_camera_position(residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 232, in _new_camera_position interpolate_camera(session, 0, frames=1) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 217, in interpolate_camera ncp, fcp = _get_clip_points(session, dist) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 360, in _get_clip_points return (o+vd*dist*0.5, o+vd*dist*1.5) UnboundLocalError: local variable 'o' referenced before assignment Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\matplotlib\cbook\\__init__.py"", line 287, in process func(*args, **kwargs) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\validation\ramaplot\ramaplot.py"", line 307, in on_pick get_stepper(self.current_model).step_to(picked_rama.residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 143, in step_to self._new_camera_position(residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 232, in _new_camera_position interpolate_camera(session, 0, frames=1) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 217, in interpolate_camera ncp, fcp = _get_clip_points(session, dist) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 360, in _get_clip_points return (o+vd*dist*0.5, o+vd*dist*1.5) UnboundLocalError: local variable 'o' referenced before assignment Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\matplotlib\cbook\\__init__.py"", line 287, in process func(*args, **kwargs) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\validation\ramaplot\ramaplot.py"", line 307, in on_pick get_stepper(self.current_model).step_to(picked_rama.residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 143, in step_to self._new_camera_position(residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 232, in _new_camera_position interpolate_camera(session, 0, frames=1) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 217, in interpolate_camera ncp, fcp = _get_clip_points(session, dist) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 360, in _get_clip_points return (o+vd*dist*0.5, o+vd*dist*1.5) UnboundLocalError: local variable 'o' referenced before assignment Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\matplotlib\cbook\\__init__.py"", line 287, in process func(*args, **kwargs) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\validation\ramaplot\ramaplot.py"", line 307, in on_pick get_stepper(self.current_model).step_to(picked_rama.residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 143, in step_to self._new_camera_position(residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 232, in _new_camera_position interpolate_camera(session, 0, frames=1) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 217, in interpolate_camera ncp, fcp = _get_clip_points(session, dist) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 360, in _get_clip_points return (o+vd*dist*0.5, o+vd*dist*1.5) UnboundLocalError: local variable 'o' referenced before assignment > view sel Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\matplotlib\cbook\\__init__.py"", line 287, in process func(*args, **kwargs) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\validation\ramaplot\ramaplot.py"", line 307, in on_pick get_stepper(self.current_model).step_to(picked_rama.residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 143, in step_to self._new_camera_position(residue) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 232, in _new_camera_position interpolate_camera(session, 0, frames=1) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 217, in interpolate_camera ncp, fcp = _get_clip_points(session, dist) File ""C:\Users\sanju\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\navigate.py"", line 360, in _get_clip_points return (o+vd*dist*0.5, o+vd*dist*1.5) UnboundLocalError: local variable 'o' referenced before assignment > view sel > show sel target ab > show #!2 models > select #1 4908 atoms, 4976 bonds, 315 residues, 1 model selected > view sel > select clear > show #3 models > hide #1 models > show #4 models Fetching G7M953 UniProt info from https://www.uniprot.org/uniprot/G7M953.xml > alphafold match G7M953 Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json 1 UniProt id does not have an AlphaFold database model: G7M953 (UniProt G7M953) AlphaFold sequence search web service failed (500) ""Internal Server Error"" https://www.rbvi.ucsf.edu/chimerax/cgi-bin/alphafold_search3_cgi.py No AlphaFold model with similar sequence for UniProt G7M953 Opened 0 AlphaFold model OpenGL version: 3.3.0 NVIDIA 531.68 OpenGL renderer: NVIDIA GeForce RTX 4080 Laptop GPU/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: es_ES.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: Alienware Model: Alienware m18 R1 OS: Microsoft Windows 11 Home (Build 22621) Memory: 34,033,319,936 MaxProcessMemory: 137,438,953,344 CPU: 32 13th Gen Intel(R) Core(TM) i9-13900HX OSLanguage: es-ES Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2022.9.24 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-Clipper: 0.19.0 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-ISOLDE: 1.5 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 comtypes: 1.1.10 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 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 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 pywin32: 303 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 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 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 WMI: 1.5.1 zipp: 3.11.0 }}} " defect closed normal Structure Prediction fixed Greg Couch all ChimeraX