id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6185 Crash calling signal handler chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3rc202111250017 (2021-11-25 00:17:48 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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All rights reserved. How to cite UCSF ChimeraX > open /Users/sacosta/MICROSCOPY/FERRITIN/NEW- > RECONSTRUCTIONS/RELION/relion.cxs Opened MD_Oct_BPA_9Aresolution.mrc as #1, grid size 250,250,250, pixel 0.832, shown at level 0.0287, step 1, values float32 Opened relion_locres.mrc as #2, grid size 250,250,250, pixel 0.832, shown at level 14.3, step 1, values float32 Opened relion_locres_filtered.mrc as #3, grid size 250,250,250, pixel 0.832, shown at level 0.0559, step 1, values float32 Map values for surface ""surface"": minimum 0.04954, mean 0.05342, maximum 0.05526 opened ChimeraX session > open /Users/sacosta/MICROSCOPY/FERRITIN/map/md-20-snapshots.pdb Chain information for md-20-snapshots.pdb --- Chain | Description 6.1/A 6.2/A 6.3/A 6.4/A 6.5/A 6.6/A 6.7/A 6.8/A 6.9/A 6.10/A 6.11/A 6.12/A 6.13/A 6.14/A 6.15/A 6.16/A 6.17/A 6.18/A 6.19/A 6.20/A | No description available 6.1/B 6.2/B 6.3/B 6.4/B 6.5/B 6.6/B 6.7/B 6.8/B 6.9/B 6.10/B 6.11/B 6.12/B 6.13/B 6.14/B 6.15/B 6.16/B 6.17/B 6.18/B 6.19/B 6.20/B 6.1/C 6.2/C 6.3/C 6.4/C 6.5/C 6.6/C 6.7/C 6.8/C 6.9/C 6.10/C 6.11/C 6.12/C 6.13/C 6.14/C 6.15/C 6.16/C 6.17/C 6.18/C 6.19/C 6.20/C 6.1/D 6.2/D 6.3/D 6.4/D 6.5/D 6.6/D 6.7/D 6.8/D 6.9/D 6.10/D 6.11/D 6.12/D 6.13/D 6.14/D 6.15/D 6.16/D 6.17/D 6.18/D 6.19/D 6.20/D 6.1/E 6.2/E 6.3/E 6.4/E 6.5/E 6.6/E 6.7/E 6.8/E 6.9/E 6.10/E 6.11/E 6.12/E 6.13/E 6.14/E 6.15/E 6.16/E 6.17/E 6.18/E 6.19/E 6.20/E 6.1/F 6.2/F 6.3/F 6.4/F 6.5/F 6.6/F 6.7/F 6.8/F 6.9/F 6.10/F 6.11/F 6.12/F 6.13/F 6.14/F 6.15/F 6.16/F 6.17/F 6.18/F 6.19/F 6.20/F 6.1/G 6.2/G 6.3/G 6.4/G 6.5/G 6.6/G 6.7/G 6.8/G 6.9/G 6.10/G 6.11/G 6.12/G 6.13/G 6.14/G 6.15/G 6.16/G 6.17/G 6.18/G 6.19/G 6.20/G 6.1/H 6.2/H 6.3/H 6.4/H 6.5/H 6.6/H 6.7/H 6.8/H 6.9/H 6.10/H 6.11/H 6.12/H 6.13/H 6.14/H 6.15/H 6.16/H 6.17/H 6.18/H 6.19/H 6.20/H 6.1/I 6.2/I 6.3/I 6.4/I 6.5/I 6.6/I 6.7/I 6.8/I 6.9/I 6.10/I 6.11/I 6.12/I 6.13/I 6.14/I 6.15/I 6.16/I 6.17/I 6.18/I 6.19/I 6.20/I 6.1/J 6.2/J 6.3/J 6.4/J 6.5/J 6.6/J 6.7/J 6.8/J 6.9/J 6.10/J 6.11/J 6.12/J 6.13/J 6.14/J 6.15/J 6.16/J 6.17/J 6.18/J 6.19/J 6.20/J 6.1/K 6.2/K 6.3/K 6.4/K 6.5/K 6.6/K 6.7/K 6.8/K 6.9/K 6.10/K 6.11/K 6.12/K 6.13/K 6.14/K 6.15/K 6.16/K 6.17/K 6.18/K 6.19/K 6.20/K 6.1/L 6.2/L 6.3/L 6.4/L 6.5/L 6.6/L 6.7/L 6.8/L 6.9/L 6.10/L 6.11/L 6.12/L 6.13/L 6.14/L 6.15/L 6.16/L 6.17/L 6.18/L 6.19/L 6.20/L 6.1/M 6.2/M 6.3/M 6.4/M 6.5/M 6.6/M 6.7/M 6.8/M 6.9/M 6.10/M 6.11/M 6.12/M 6.13/M 6.14/M 6.15/M 6.16/M 6.17/M 6.18/M 6.19/M 6.20/M 6.1/N 6.2/N 6.3/N 6.4/N 6.5/N 6.6/N 6.7/N 6.8/N 6.9/N 6.10/N 6.11/N 6.12/N 6.13/N 6.14/N 6.15/N 6.16/N 6.17/N 6.18/N 6.19/N 6.20/N 6.1/O 6.2/O 6.3/O 6.4/O 6.5/O 6.6/O 6.7/O 6.8/O 6.9/O 6.10/O 6.11/O 6.12/O 6.13/O 6.14/O 6.15/O 6.16/O 6.17/O 6.18/O 6.19/O 6.20/O 6.1/P 6.2/P 6.3/P 6.4/P 6.5/P 6.6/P 6.7/P 6.8/P 6.9/P 6.10/P 6.11/P 6.12/P 6.13/P 6.14/P 6.15/P 6.16/P 6.17/P 6.18/P 6.19/P 6.20/P 6.1/Q 6.2/Q 6.3/Q 6.4/Q 6.5/Q 6.6/Q 6.7/Q 6.8/Q 6.9/Q 6.10/Q 6.11/Q 6.12/Q 6.13/Q 6.14/Q 6.15/Q 6.16/Q 6.17/Q 6.18/Q 6.19/Q 6.20/Q 6.1/R 6.2/R 6.3/R 6.4/R 6.5/R 6.6/R 6.7/R 6.8/R 6.9/R 6.10/R 6.11/R 6.12/R 6.13/R 6.14/R 6.15/R 6.16/R 6.17/R 6.18/R 6.19/R 6.20/R 6.1/S 6.2/S 6.3/S 6.4/S 6.5/S 6.6/S 6.7/S 6.8/S 6.9/S 6.10/S 6.11/S 6.12/S 6.13/S 6.14/S 6.15/S 6.16/S 6.17/S 6.18/S 6.19/S 6.20/S 6.1/T 6.2/T 6.3/T 6.4/T 6.5/T 6.6/T 6.7/T 6.8/T 6.9/T 6.10/T 6.11/T 6.12/T 6.13/T 6.14/T 6.15/T 6.16/T 6.17/T 6.18/T 6.19/T 6.20/T 6.1/U 6.2/U 6.3/U 6.4/U 6.5/U 6.6/U 6.7/U 6.8/U 6.9/U 6.10/U 6.11/U 6.12/U 6.13/U 6.14/U 6.15/U 6.16/U 6.17/U 6.18/U 6.19/U 6.20/U 6.1/V 6.2/V 6.3/V 6.4/V 6.5/V 6.6/V 6.7/V 6.8/V 6.9/V 6.10/V 6.11/V 6.12/V 6.13/V 6.14/V 6.15/V 6.16/V 6.17/V 6.18/V 6.19/V 6.20/V 6.1/W 6.2/W 6.3/W 6.4/W 6.5/W 6.6/W 6.7/W 6.8/W 6.9/W 6.10/W 6.11/W 6.12/W 6.13/W 6.14/W 6.15/W 6.16/W 6.17/W 6.18/W 6.19/W 6.20/W 6.1/X 6.2/X 6.3/X 6.4/X 6.5/X 6.6/X 6.7/X 6.8/X 6.9/X 6.10/X 6.11/X 6.12/X 6.13/X 6.14/X 6.15/X 6.16/X 6.17/X 6.18/X 6.19/X 6.20/X | No description available > ui tool show H-Bonds > ui tool show Matchmaker > matchmaker #6.1-20 to #4/A pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain A (#6.1), sequence alignment score = 868.1 RMSD between 163 pruned atom pairs is 1.018 angstroms; (across all 169 pairs: 1.101) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain L (#6.2), sequence alignment score = 871.5 RMSD between 165 pruned atom pairs is 0.841 angstroms; (across all 170 pairs: 0.927) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain D (#6.3), sequence alignment score = 867.9 RMSD between 166 pruned atom pairs is 0.810 angstroms; (across all 170 pairs: 0.869) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain I (#6.4), sequence alignment score = 868.5 RMSD between 168 pruned atom pairs is 0.825 angstroms; (across all 170 pairs: 0.882) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain L (#6.5), sequence alignment score = 864.9 RMSD between 165 pruned atom pairs is 0.769 angstroms; (across all 170 pairs: 0.913) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain Q (#6.6), sequence alignment score = 869.1 RMSD between 163 pruned atom pairs is 0.805 angstroms; (across all 170 pairs: 0.979) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain L (#6.7), sequence alignment score = 871.5 RMSD between 163 pruned atom pairs is 0.647 angstroms; (across all 170 pairs: 0.894) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain L (#6.8), sequence alignment score = 871.5 RMSD between 167 pruned atom pairs is 0.813 angstroms; (across all 170 pairs: 0.928) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain I (#6.9), sequence alignment score = 868.5 RMSD between 166 pruned atom pairs is 0.649 angstroms; (across all 170 pairs: 0.783) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain M (#6.10), sequence alignment score = 875.1 RMSD between 147 pruned atom pairs is 0.952 angstroms; (across all 170 pairs: 1.373) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain P (#6.11), sequence alignment score = 869.1 RMSD between 163 pruned atom pairs is 0.857 angstroms; (across all 170 pairs: 1.050) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain V (#6.12), sequence alignment score = 871.5 RMSD between 167 pruned atom pairs is 0.671 angstroms; (across all 170 pairs: 0.797) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain I (#6.13), sequence alignment score = 868.5 RMSD between 168 pruned atom pairs is 0.654 angstroms; (across all 170 pairs: 0.767) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain D (#6.14), sequence alignment score = 865.5 RMSD between 149 pruned atom pairs is 0.915 angstroms; (across all 170 pairs: 1.477) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain I (#6.15), sequence alignment score = 872.1 RMSD between 168 pruned atom pairs is 0.676 angstroms; (across all 170 pairs: 0.739) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain M (#6.16), sequence alignment score = 869.1 RMSD between 155 pruned atom pairs is 0.868 angstroms; (across all 170 pairs: 1.227) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain B (#6.17), sequence alignment score = 867.9 RMSD between 165 pruned atom pairs is 0.647 angstroms; (across all 170 pairs: 0.852) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain M (#6.18), sequence alignment score = 872.1 RMSD between 163 pruned atom pairs is 0.914 angstroms; (across all 170 pairs: 1.160) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain P (#6.19), sequence alignment score = 869.1 RMSD between 166 pruned atom pairs is 0.714 angstroms; (across all 170 pairs: 0.873) Matchmaker ferritin.pdb, chain A (#4) with md-20-snapshots.pdb, chain G (#6.20), sequence alignment score = 868.5 RMSD between 163 pruned atom pairs is 0.682 angstroms; (across all 170 pairs: 0.889) > select #6 655080 atoms, 665640 bonds, 81580 residues, 21 models selected > hide sel atoms > show sel cartoons > select helix 513448 atoms, 519051 bonds, 63893 residues, 21 models selected > hide sel cartoons > close #6 > select /A 32736 atoms, 33264 bonds, 23 pseudobonds, 4080 residues, 2 models selected > show sel cartoons > open /Users/sacosta/MICROSCOPY/FERRITIN/map/rmsd-60-snapshots-not-align.dat Install the SEQCROW bundle to open ""Psi4 output file"" format files. Opener for format 'Psi4 output file' is not installed; see log for more info > open /Users/sacosta/MICROSCOPY/FERRITIN/map/md-60snapshots.pdb Chain information for md-60snapshots.pdb --- Chain | Description 6.1/A 6.2/A 6.3/A 6.4/A 6.5/A 6.6/A 6.7/A 6.8/A 6.9/A 6.10/A 6.11/A 6.12/A 6.13/A 6.14/A 6.15/A 6.16/A 6.17/A 6.18/A 6.19/A 6.20/A 6.21/A 6.22/A 6.23/A 6.24/A 6.25/A 6.26/A 6.27/A 6.28/A 6.29/A 6.30/A 6.31/A 6.32/A 6.33/A 6.34/A 6.35/A 6.36/A 6.37/A 6.38/A 6.39/A 6.40/A 6.41/A 6.42/A 6.43/A 6.44/A 6.45/A 6.46/A 6.47/A 6.48/A 6.49/A 6.50/A 6.51/A 6.52/A 6.53/A 6.54/A 6.55/A 6.56/A 6.57/A 6.58/A 6.59/A 6.60/A 6.61/A | No description available 6.1/B 6.2/B 6.3/B 6.4/B 6.5/B 6.6/B 6.7/B 6.8/B 6.9/B 6.10/B 6.11/B 6.12/B 6.13/B 6.14/B 6.15/B 6.16/B 6.17/B 6.18/B 6.19/B 6.20/B 6.21/B 6.22/B 6.23/B 6.24/B 6.25/B 6.26/B 6.27/B 6.28/B 6.29/B 6.30/B 6.31/B 6.32/B 6.33/B 6.34/B 6.35/B 6.36/B 6.37/B 6.38/B 6.39/B 6.40/B 6.41/B 6.42/B 6.43/B 6.44/B 6.45/B 6.46/B 6.47/B 6.48/B 6.49/B 6.50/B 6.51/B 6.52/B 6.53/B 6.54/B 6.55/B 6.56/B 6.57/B 6.58/B 6.59/B 6.60/B 6.61/B 6.1/C 6.2/C 6.3/C 6.4/C 6.5/C 6.6/C 6.7/C 6.8/C 6.9/C 6.10/C 6.11/C 6.12/C 6.13/C 6.14/C 6.15/C 6.16/C 6.17/C 6.18/C 6.19/C 6.20/C 6.21/C 6.22/C 6.23/C 6.24/C 6.25/C 6.26/C 6.27/C 6.28/C 6.29/C 6.30/C 6.31/C 6.32/C 6.33/C 6.34/C 6.35/C 6.36/C 6.37/C 6.38/C 6.39/C 6.40/C 6.41/C 6.42/C 6.43/C 6.44/C 6.45/C 6.46/C 6.47/C 6.48/C 6.49/C 6.50/C 6.51/C 6.52/C 6.53/C 6.54/C 6.55/C 6.56/C 6.57/C 6.58/C 6.59/C 6.60/C 6.61/C 6.1/D 6.2/D 6.3/D 6.4/D 6.5/D 6.6/D 6.7/D 6.8/D 6.9/D 6.10/D 6.11/D 6.12/D 6.13/D 6.14/D 6.15/D 6.16/D 6.17/D 6.18/D 6.19/D 6.20/D 6.21/D 6.22/D 6.23/D 6.24/D 6.25/D 6.26/D 6.27/D 6.28/D 6.29/D 6.30/D 6.31/D 6.32/D 6.33/D 6.34/D 6.35/D 6.36/D 6.37/D 6.38/D 6.39/D 6.40/D 6.41/D 6.42/D 6.43/D 6.44/D 6.45/D 6.46/D 6.47/D 6.48/D 6.49/D 6.50/D 6.51/D 6.52/D 6.53/D 6.54/D 6.55/D 6.56/D 6.57/D 6.58/D 6.59/D 6.60/D 6.61/D 6.1/E 6.2/E 6.3/E 6.4/E 6.5/E 6.6/E 6.7/E 6.8/E 6.9/E 6.10/E 6.11/E 6.12/E 6.13/E 6.14/E 6.15/E 6.16/E 6.17/E 6.18/E 6.19/E 6.20/E 6.21/E 6.22/E 6.23/E 6.24/E 6.25/E 6.26/E 6.27/E 6.28/E 6.29/E 6.30/E 6.31/E 6.32/E 6.33/E 6.34/E 6.35/E 6.36/E 6.37/E 6.38/E 6.39/E 6.40/E 6.41/E 6.42/E 6.43/E 6.44/E 6.45/E 6.46/E 6.47/E 6.48/E 6.49/E 6.50/E 6.51/E 6.52/E 6.53/E 6.54/E 6.55/E 6.56/E 6.57/E 6.58/E 6.59/E 6.60/E 6.61/E 6.1/F 6.2/F 6.3/F 6.4/F 6.5/F 6.6/F 6.7/F 6.8/F 6.9/F 6.10/F 6.11/F 6.12/F 6.13/F 6.14/F 6.15/F 6.16/F 6.17/F 6.18/F 6.19/F 6.20/F 6.21/F 6.22/F 6.23/F 6.24/F 6.25/F 6.26/F 6.27/F 6.28/F 6.29/F 6.30/F 6.31/F 6.32/F 6.33/F 6.34/F 6.35/F 6.36/F 6.37/F 6.38/F 6.39/F 6.40/F 6.41/F 6.42/F 6.43/F 6.44/F 6.45/F 6.46/F 6.47/F 6.48/F 6.49/F 6.50/F 6.51/F 6.52/F 6.53/F 6.54/F 6.55/F 6.56/F 6.57/F 6.58/F 6.59/F 6.60/F 6.61/F 6.1/G 6.2/G 6.3/G 6.4/G 6.5/G 6.6/G 6.7/G 6.8/G 6.9/G 6.10/G 6.11/G 6.12/G 6.13/G 6.14/G 6.15/G 6.16/G 6.17/G 6.18/G 6.19/G 6.20/G 6.21/G 6.22/G 6.23/G 6.24/G 6.25/G 6.26/G 6.27/G 6.28/G 6.29/G 6.30/G 6.31/G 6.32/G 6.33/G 6.34/G 6.35/G 6.36/G 6.37/G 6.38/G 6.39/G 6.40/G 6.41/G 6.42/G 6.43/G 6.44/G 6.45/G 6.46/G 6.47/G 6.48/G 6.49/G 6.50/G 6.51/G 6.52/G 6.53/G 6.54/G 6.55/G 6.56/G 6.57/G 6.58/G 6.59/G 6.60/G 6.61/G 6.1/H 6.2/H 6.3/H 6.4/H 6.5/H 6.6/H 6.7/H 6.8/H 6.9/H 6.10/H 6.11/H 6.12/H 6.13/H 6.14/H 6.15/H 6.16/H 6.17/H 6.18/H 6.19/H 6.20/H 6.21/H 6.22/H 6.23/H 6.24/H 6.25/H 6.26/H 6.27/H 6.28/H 6.29/H 6.30/H 6.31/H 6.32/H 6.33/H 6.34/H 6.35/H 6.36/H 6.37/H 6.38/H 6.39/H 6.40/H 6.41/H 6.42/H 6.43/H 6.44/H 6.45/H 6.46/H 6.47/H 6.48/H 6.49/H 6.50/H 6.51/H 6.52/H 6.53/H 6.54/H 6.55/H 6.56/H 6.57/H 6.58/H 6.59/H 6.60/H 6.61/H 6.1/I 6.2/I 6.3/I 6.4/I 6.5/I 6.6/I 6.7/I 6.8/I 6.9/I 6.10/I 6.11/I 6.12/I 6.13/I 6.14/I 6.15/I 6.16/I 6.17/I 6.18/I 6.19/I 6.20/I 6.21/I 6.22/I 6.23/I 6.24/I 6.25/I 6.26/I 6.27/I 6.28/I 6.29/I 6.30/I 6.31/I 6.32/I 6.33/I 6.34/I 6.35/I 6.36/I 6.37/I 6.38/I 6.39/I 6.40/I 6.41/I 6.42/I 6.43/I 6.44/I 6.45/I 6.46/I 6.47/I 6.48/I 6.49/I 6.50/I 6.51/I 6.52/I 6.53/I 6.54/I 6.55/I 6.56/I 6.57/I 6.58/I 6.59/I 6.60/I 6.61/I 6.1/J 6.2/J 6.3/J 6.4/J 6.5/J 6.6/J 6.7/J 6.8/J 6.9/J 6.10/J 6.11/J 6.12/J 6.13/J 6.14/J 6.15/J 6.16/J 6.17/J 6.18/J 6.19/J 6.20/J 6.21/J 6.22/J 6.23/J 6.24/J 6.25/J 6.26/J 6.27/J 6.28/J 6.29/J 6.30/J 6.31/J 6.32/J 6.33/J 6.34/J 6.35/J 6.36/J 6.37/J 6.38/J 6.39/J 6.40/J 6.41/J 6.42/J 6.43/J 6.44/J 6.45/J 6.46/J 6.47/J 6.48/J 6.49/J 6.50/J 6.51/J 6.52/J 6.53/J 6.54/J 6.55/J 6.56/J 6.57/J 6.58/J 6.59/J 6.60/J 6.61/J 6.1/K 6.2/K 6.3/K 6.4/K 6.5/K 6.6/K 6.7/K 6.8/K 6.9/K 6.10/K 6.11/K 6.12/K 6.13/K 6.14/K 6.15/K 6.16/K 6.17/K 6.18/K 6.19/K 6.20/K 6.21/K 6.22/K 6.23/K 6.24/K 6.25/K 6.26/K 6.27/K 6.28/K 6.29/K 6.30/K 6.31/K 6.32/K 6.33/K 6.34/K 6.35/K 6.36/K 6.37/K 6.38/K 6.39/K 6.40/K 6.41/K 6.42/K 6.43/K 6.44/K 6.45/K 6.46/K 6.47/K 6.48/K 6.49/K 6.50/K 6.51/K 6.52/K 6.53/K 6.54/K 6.55/K 6.56/K 6.57/K 6.58/K 6.59/K 6.60/K 6.61/K 6.1/L 6.2/L 6.3/L 6.4/L 6.5/L 6.6/L 6.7/L 6.8/L 6.9/L 6.10/L 6.11/L 6.12/L 6.13/L 6.14/L 6.15/L 6.16/L 6.17/L 6.18/L 6.19/L 6.20/L 6.21/L 6.22/L 6.23/L 6.24/L 6.25/L 6.26/L 6.27/L 6.28/L 6.29/L 6.30/L 6.31/L 6.32/L 6.33/L 6.34/L 6.35/L 6.36/L 6.37/L 6.38/L 6.39/L 6.40/L 6.41/L 6.42/L 6.43/L 6.44/L 6.45/L 6.46/L 6.47/L 6.48/L 6.49/L 6.50/L 6.51/L 6.52/L 6.53/L 6.54/L 6.55/L 6.56/L 6.57/L 6.58/L 6.59/L 6.60/L 6.61/L 6.1/M 6.2/M 6.3/M 6.4/M 6.5/M 6.6/M 6.7/M 6.8/M 6.9/M 6.10/M 6.11/M 6.12/M 6.13/M 6.14/M 6.15/M 6.16/M 6.17/M 6.18/M 6.19/M 6.20/M 6.21/M 6.22/M 6.23/M 6.24/M 6.25/M 6.26/M 6.27/M 6.28/M 6.29/M 6.30/M 6.31/M 6.32/M 6.33/M 6.34/M 6.35/M 6.36/M 6.37/M 6.38/M 6.39/M 6.40/M 6.41/M 6.42/M 6.43/M 6.44/M 6.45/M 6.46/M 6.47/M 6.48/M 6.49/M 6.50/M 6.51/M 6.52/M 6.53/M 6.54/M 6.55/M 6.56/M 6.57/M 6.58/M 6.59/M 6.60/M 6.61/M 6.1/N 6.2/N 6.3/N 6.4/N 6.5/N 6.6/N 6.7/N 6.8/N 6.9/N 6.10/N 6.11/N 6.12/N 6.13/N 6.14/N 6.15/N 6.16/N 6.17/N 6.18/N 6.19/N 6.20/N 6.21/N 6.22/N 6.23/N 6.24/N 6.25/N 6.26/N 6.27/N 6.28/N 6.29/N 6.30/N 6.31/N 6.32/N 6.33/N 6.34/N 6.35/N 6.36/N 6.37/N 6.38/N 6.39/N 6.40/N 6.41/N 6.42/N 6.43/N 6.44/N 6.45/N 6.46/N 6.47/N 6.48/N 6.49/N 6.50/N 6.51/N 6.52/N 6.53/N 6.54/N 6.55/N 6.56/N 6.57/N 6.58/N 6.59/N 6.60/N 6.61/N 6.1/O 6.2/O 6.3/O 6.4/O 6.5/O 6.6/O 6.7/O 6.8/O 6.9/O 6.10/O 6.11/O 6.12/O 6.13/O 6.14/O 6.15/O 6.16/O 6.17/O 6.18/O 6.19/O 6.20/O 6.21/O 6.22/O 6.23/O 6.24/O 6.25/O 6.26/O 6.27/O 6.28/O 6.29/O 6.30/O 6.31/O 6.32/O 6.33/O 6.34/O 6.35/O 6.36/O 6.37/O 6.38/O 6.39/O 6.40/O 6.41/O 6.42/O 6.43/O 6.44/O 6.45/O 6.46/O 6.47/O 6.48/O 6.49/O 6.50/O 6.51/O 6.52/O 6.53/O 6.54/O 6.55/O 6.56/O 6.57/O 6.58/O 6.59/O 6.60/O 6.61/O 6.1/P 6.2/P 6.3/P 6.4/P 6.5/P 6.6/P 6.7/P 6.8/P 6.9/P 6.10/P 6.11/P 6.12/P 6.13/P 6.14/P 6.15/P 6.16/P 6.17/P 6.18/P 6.19/P 6.20/P 6.21/P 6.22/P 6.23/P 6.24/P 6.25/P 6.26/P 6.27/P 6.28/P 6.29/P 6.30/P 6.31/P 6.32/P 6.33/P 6.34/P 6.35/P 6.36/P 6.37/P 6.38/P 6.39/P 6.40/P 6.41/P 6.42/P 6.43/P 6.44/P 6.45/P 6.46/P 6.47/P 6.48/P 6.49/P 6.50/P 6.51/P 6.52/P 6.53/P 6.54/P 6.55/P 6.56/P 6.57/P 6.58/P 6.59/P 6.60/P 6.61/P 6.1/Q 6.2/Q 6.3/Q 6.4/Q 6.5/Q 6.6/Q 6.7/Q 6.8/Q 6.9/Q 6.10/Q 6.11/Q 6.12/Q 6.13/Q 6.14/Q 6.15/Q 6.16/Q 6.17/Q 6.18/Q 6.19/Q 6.20/Q 6.21/Q 6.22/Q 6.23/Q 6.24/Q 6.25/Q 6.26/Q 6.27/Q 6.28/Q 6.29/Q 6.30/Q 6.31/Q 6.32/Q 6.33/Q 6.34/Q 6.35/Q 6.36/Q 6.37/Q 6.38/Q 6.39/Q 6.40/Q 6.41/Q 6.42/Q 6.43/Q 6.44/Q 6.45/Q 6.46/Q 6.47/Q 6.48/Q 6.49/Q 6.50/Q 6.51/Q 6.52/Q 6.53/Q 6.54/Q 6.55/Q 6.56/Q 6.57/Q 6.58/Q 6.59/Q 6.60/Q 6.61/Q 6.1/R 6.2/R 6.3/R 6.4/R 6.5/R 6.6/R 6.7/R 6.8/R 6.9/R 6.10/R 6.11/R 6.12/R 6.13/R 6.14/R 6.15/R 6.16/R 6.17/R 6.18/R 6.19/R 6.20/R 6.21/R 6.22/R 6.23/R 6.24/R 6.25/R 6.26/R 6.27/R 6.28/R 6.29/R 6.30/R 6.31/R 6.32/R 6.33/R 6.34/R 6.35/R 6.36/R 6.37/R 6.38/R 6.39/R 6.40/R 6.41/R 6.42/R 6.43/R 6.44/R 6.45/R 6.46/R 6.47/R 6.48/R 6.49/R 6.50/R 6.51/R 6.52/R 6.53/R 6.54/R 6.55/R 6.56/R 6.57/R 6.58/R 6.59/R 6.60/R 6.61/R 6.1/S 6.2/S 6.3/S 6.4/S 6.5/S 6.6/S 6.7/S 6.8/S 6.9/S 6.10/S 6.11/S 6.12/S 6.13/S 6.14/S 6.15/S 6.16/S 6.17/S 6.18/S 6.19/S 6.20/S 6.21/S 6.22/S 6.23/S 6.24/S 6.25/S 6.26/S 6.27/S 6.28/S 6.29/S 6.30/S 6.31/S 6.32/S 6.33/S 6.34/S 6.35/S 6.36/S 6.37/S 6.38/S 6.39/S 6.40/S 6.41/S 6.42/S 6.43/S 6.44/S 6.45/S 6.46/S 6.47/S 6.48/S 6.49/S 6.50/S 6.51/S 6.52/S 6.53/S 6.54/S 6.55/S 6.56/S 6.57/S 6.58/S 6.59/S 6.60/S 6.61/S 6.1/T 6.2/T 6.3/T 6.4/T 6.5/T 6.6/T 6.7/T 6.8/T 6.9/T 6.10/T 6.11/T 6.12/T 6.13/T 6.14/T 6.15/T 6.16/T 6.17/T 6.18/T 6.19/T 6.20/T 6.21/T 6.22/T 6.23/T 6.24/T 6.25/T 6.26/T 6.27/T 6.28/T 6.29/T 6.30/T 6.31/T 6.32/T 6.33/T 6.34/T 6.35/T 6.36/T 6.37/T 6.38/T 6.39/T 6.40/T 6.41/T 6.42/T 6.43/T 6.44/T 6.45/T 6.46/T 6.47/T 6.48/T 6.49/T 6.50/T 6.51/T 6.52/T 6.53/T 6.54/T 6.55/T 6.56/T 6.57/T 6.58/T 6.59/T 6.60/T 6.61/T 6.1/U 6.2/U 6.3/U 6.4/U 6.5/U 6.6/U 6.7/U 6.8/U 6.9/U 6.10/U 6.11/U 6.12/U 6.13/U 6.14/U 6.15/U 6.16/U 6.17/U 6.18/U 6.19/U 6.20/U 6.21/U 6.22/U 6.23/U 6.24/U 6.25/U 6.26/U 6.27/U 6.28/U 6.29/U 6.30/U 6.31/U 6.32/U 6.33/U 6.34/U 6.35/U 6.36/U 6.37/U 6.38/U 6.39/U 6.40/U 6.41/U 6.42/U 6.43/U 6.44/U 6.45/U 6.46/U 6.47/U 6.48/U 6.49/U 6.50/U 6.51/U 6.52/U 6.53/U 6.54/U 6.55/U 6.56/U 6.57/U 6.58/U 6.59/U 6.60/U 6.61/U 6.1/V 6.2/V 6.3/V 6.4/V 6.5/V 6.6/V 6.7/V 6.8/V 6.9/V 6.10/V 6.11/V 6.12/V 6.13/V 6.14/V 6.15/V 6.16/V 6.17/V 6.18/V 6.19/V 6.20/V 6.21/V 6.22/V 6.23/V 6.24/V 6.25/V 6.26/V 6.27/V 6.28/V 6.29/V 6.30/V 6.31/V 6.32/V 6.33/V 6.34/V 6.35/V 6.36/V 6.37/V 6.38/V 6.39/V 6.40/V 6.41/V 6.42/V 6.43/V 6.44/V 6.45/V 6.46/V 6.47/V 6.48/V 6.49/V 6.50/V 6.51/V 6.52/V 6.53/V 6.54/V 6.55/V 6.56/V 6.57/V 6.58/V 6.59/V 6.60/V 6.61/V 6.1/W 6.2/W 6.3/W 6.4/W 6.5/W 6.6/W 6.7/W 6.8/W 6.9/W 6.10/W 6.11/W 6.12/W 6.13/W 6.14/W 6.15/W 6.16/W 6.17/W 6.18/W 6.19/W 6.20/W 6.21/W 6.22/W 6.23/W 6.24/W 6.25/W 6.26/W 6.27/W 6.28/W 6.29/W 6.30/W 6.31/W 6.32/W 6.33/W 6.34/W 6.35/W 6.36/W 6.37/W 6.38/W 6.39/W 6.40/W 6.41/W 6.42/W 6.43/W 6.44/W 6.45/W 6.46/W 6.47/W 6.48/W 6.49/W 6.50/W 6.51/W 6.52/W 6.53/W 6.54/W 6.55/W 6.56/W 6.57/W 6.58/W 6.59/W 6.60/W 6.61/W 6.1/X 6.2/X 6.3/X 6.4/X 6.5/X 6.6/X 6.7/X 6.8/X 6.9/X 6.10/X 6.11/X 6.12/X 6.13/X 6.14/X 6.15/X 6.16/X 6.17/X 6.18/X 6.19/X 6.20/X 6.21/X 6.22/X 6.23/X 6.24/X 6.25/X 6.26/X 6.27/X 6.28/X 6.29/X 6.30/X 6.31/X 6.32/X 6.33/X 6.34/X 6.35/X 6.36/X 6.37/X 6.38/X 6.39/X 6.40/X 6.41/X 6.42/X 6.43/X 6.44/X 6.45/X 6.46/X 6.47/X 6.48/X 6.49/X 6.50/X 6.51/X 6.52/X 6.53/X 6.54/X 6.55/X 6.56/X 6.57/X 6.58/X 6.59/X 6.60/X 6.61/X | No description available > select #6 1997994 atoms, 2030202 bonds, 248819 residues, 62 models selected > ui tool show Matchmaker > matchmaker #6.1-61 to #4/A pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain D (#6.1), sequence alignment score = 867.9 RMSD between 168 pruned atom pairs is 0.712 angstroms; (across all 170 pairs: 0.765) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain D (#6.2), sequence alignment score = 867.9 RMSD between 168 pruned atom pairs is 0.712 angstroms; (across all 170 pairs: 0.765) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain V (#6.3), sequence alignment score = 871.5 RMSD between 169 pruned atom pairs is 0.626 angstroms; (across all 170 pairs: 0.654) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain A (#6.4), sequence alignment score = 868.1 RMSD between 163 pruned atom pairs is 1.018 angstroms; (across all 169 pairs: 1.101) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain D (#6.5), sequence alignment score = 867.9 RMSD between 167 pruned atom pairs is 0.799 angstroms; (across all 170 pairs: 0.862) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain L (#6.6), sequence alignment score = 864.9 RMSD between 166 pruned atom pairs is 0.877 angstroms; (across all 170 pairs: 0.940) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain L (#6.7), sequence alignment score = 871.5 RMSD between 165 pruned atom pairs is 0.841 angstroms; (across all 170 pairs: 0.927) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain D (#6.8), sequence alignment score = 868.5 RMSD between 167 pruned atom pairs is 0.776 angstroms; (across all 170 pairs: 0.822) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain C (#6.9), sequence alignment score = 868.5 RMSD between 162 pruned atom pairs is 0.721 angstroms; (across all 170 pairs: 0.980) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain D (#6.10), sequence alignment score = 867.9 RMSD between 166 pruned atom pairs is 0.810 angstroms; (across all 170 pairs: 0.869) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain I (#6.11), sequence alignment score = 875.1 RMSD between 170 pruned atom pairs is 0.655 angstroms; (across all 170 pairs: 0.655) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain L (#6.12), sequence alignment score = 872.1 RMSD between 165 pruned atom pairs is 0.755 angstroms; (across all 170 pairs: 0.903) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain I (#6.13), sequence alignment score = 868.5 RMSD between 168 pruned atom pairs is 0.825 angstroms; (across all 170 pairs: 0.882) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain L (#6.14), sequence alignment score = 869.1 RMSD between 167 pruned atom pairs is 0.692 angstroms; (across all 170 pairs: 0.829) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain O (#6.15), sequence alignment score = 875.1 RMSD between 162 pruned atom pairs is 0.680 angstroms; (across all 170 pairs: 0.962) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain L (#6.16), sequence alignment score = 864.9 RMSD between 165 pruned atom pairs is 0.769 angstroms; (across all 170 pairs: 0.913) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain L (#6.17), sequence alignment score = 869.1 RMSD between 164 pruned atom pairs is 0.770 angstroms; (across all 170 pairs: 0.941) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain J (#6.18), sequence alignment score = 867.9 RMSD between 169 pruned atom pairs is 0.678 angstroms; (across all 170 pairs: 0.730) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain Q (#6.19), sequence alignment score = 869.1 RMSD between 163 pruned atom pairs is 0.805 angstroms; (across all 170 pairs: 0.979) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain M (#6.20), sequence alignment score = 872.1 RMSD between 164 pruned atom pairs is 0.868 angstroms; (across all 170 pairs: 1.059) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain W (#6.21), sequence alignment score = 867.9 RMSD between 168 pruned atom pairs is 0.788 angstroms; (across all 170 pairs: 0.852) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain L (#6.22), sequence alignment score = 871.5 RMSD between 163 pruned atom pairs is 0.647 angstroms; (across all 170 pairs: 0.894) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain I (#6.23), sequence alignment score = 875.1 RMSD between 167 pruned atom pairs is 0.591 angstroms; (across all 170 pairs: 0.724) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain E (#6.24), sequence alignment score = 872.1 RMSD between 166 pruned atom pairs is 0.751 angstroms; (across all 170 pairs: 0.869) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain L (#6.25), sequence alignment score = 871.5 RMSD between 167 pruned atom pairs is 0.813 angstroms; (across all 170 pairs: 0.928) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain G (#6.26), sequence alignment score = 871.5 RMSD between 166 pruned atom pairs is 0.684 angstroms; (across all 170 pairs: 0.812) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain I (#6.27), sequence alignment score = 871.5 RMSD between 168 pruned atom pairs is 0.726 angstroms; (across all 170 pairs: 0.798) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain I (#6.28), sequence alignment score = 868.5 RMSD between 166 pruned atom pairs is 0.649 angstroms; (across all 170 pairs: 0.783) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain F (#6.29), sequence alignment score = 868.5 RMSD between 164 pruned atom pairs is 0.654 angstroms; (across all 170 pairs: 0.980) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain I (#6.30), sequence alignment score = 868.5 RMSD between 165 pruned atom pairs is 0.782 angstroms; (across all 170 pairs: 0.925) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain M (#6.31), sequence alignment score = 875.1 RMSD between 147 pruned atom pairs is 0.952 angstroms; (across all 170 pairs: 1.373) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain M (#6.32), sequence alignment score = 868.5 RMSD between 164 pruned atom pairs is 0.912 angstroms; (across all 170 pairs: 1.084) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain I (#6.33), sequence alignment score = 869.1 RMSD between 166 pruned atom pairs is 0.678 angstroms; (across all 170 pairs: 0.839) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain P (#6.34), sequence alignment score = 869.1 RMSD between 163 pruned atom pairs is 0.857 angstroms; (across all 170 pairs: 1.050) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain L (#6.35), sequence alignment score = 871.5 RMSD between 165 pruned atom pairs is 0.702 angstroms; (across all 170 pairs: 0.889) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain I (#6.36), sequence alignment score = 871.5 RMSD between 168 pruned atom pairs is 0.729 angstroms; (across all 170 pairs: 0.815) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain V (#6.37), sequence alignment score = 871.5 RMSD between 167 pruned atom pairs is 0.671 angstroms; (across all 170 pairs: 0.797) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain B (#6.38), sequence alignment score = 868.5 RMSD between 167 pruned atom pairs is 0.632 angstroms; (across all 170 pairs: 0.744) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain O (#6.39), sequence alignment score = 871.5 RMSD between 169 pruned atom pairs is 0.664 angstroms; (across all 170 pairs: 0.719) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain I (#6.40), sequence alignment score = 868.5 RMSD between 168 pruned atom pairs is 0.654 angstroms; (across all 170 pairs: 0.767) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain B (#6.41), sequence alignment score = 868.5 RMSD between 166 pruned atom pairs is 0.634 angstroms; (across all 170 pairs: 0.795) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain L (#6.42), sequence alignment score = 869.1 RMSD between 164 pruned atom pairs is 0.613 angstroms; (across all 170 pairs: 0.830) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain D (#6.43), sequence alignment score = 865.5 RMSD between 149 pruned atom pairs is 0.915 angstroms; (across all 170 pairs: 1.477) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain L (#6.44), sequence alignment score = 872.1 RMSD between 163 pruned atom pairs is 0.652 angstroms; (across all 170 pairs: 0.901) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain I (#6.45), sequence alignment score = 867.9 RMSD between 166 pruned atom pairs is 0.657 angstroms; (across all 170 pairs: 0.807) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain I (#6.46), sequence alignment score = 872.1 RMSD between 168 pruned atom pairs is 0.676 angstroms; (across all 170 pairs: 0.739) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain L (#6.47), sequence alignment score = 865.5 RMSD between 168 pruned atom pairs is 0.675 angstroms; (across all 170 pairs: 0.751) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain I (#6.48), sequence alignment score = 871.5 RMSD between 168 pruned atom pairs is 0.624 angstroms; (across all 170 pairs: 0.711) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain M (#6.49), sequence alignment score = 869.1 RMSD between 155 pruned atom pairs is 0.868 angstroms; (across all 170 pairs: 1.227) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain M (#6.50), sequence alignment score = 872.1 RMSD between 160 pruned atom pairs is 0.892 angstroms; (across all 170 pairs: 1.133) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain M (#6.51), sequence alignment score = 872.1 RMSD between 163 pruned atom pairs is 0.903 angstroms; (across all 170 pairs: 1.101) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain B (#6.52), sequence alignment score = 867.9 RMSD between 165 pruned atom pairs is 0.647 angstroms; (across all 170 pairs: 0.852) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain L (#6.53), sequence alignment score = 872.1 RMSD between 165 pruned atom pairs is 0.655 angstroms; (across all 170 pairs: 0.844) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain B (#6.54), sequence alignment score = 875.1 RMSD between 165 pruned atom pairs is 0.583 angstroms; (across all 170 pairs: 0.783) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain M (#6.55), sequence alignment score = 872.1 RMSD between 163 pruned atom pairs is 0.914 angstroms; (across all 170 pairs: 1.160) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain M (#6.56), sequence alignment score = 869.1 RMSD between 163 pruned atom pairs is 0.841 angstroms; (across all 170 pairs: 1.000) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain F (#6.57), sequence alignment score = 875.1 RMSD between 164 pruned atom pairs is 0.729 angstroms; (across all 170 pairs: 0.937) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain P (#6.58), sequence alignment score = 869.1 RMSD between 166 pruned atom pairs is 0.714 angstroms; (across all 170 pairs: 0.873) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain M (#6.59), sequence alignment score = 872.1 RMSD between 163 pruned atom pairs is 0.896 angstroms; (across all 170 pairs: 1.122) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain F (#6.60), sequence alignment score = 871.5 RMSD between 164 pruned atom pairs is 0.759 angstroms; (across all 170 pairs: 0.990) Matchmaker ferritin.pdb, chain A (#4) with md-60snapshots.pdb, chain G (#6.61), sequence alignment score = 868.5 RMSD between 163 pruned atom pairs is 0.682 angstroms; (across all 170 pairs: 0.889) > hide sel atoms > show sel cartoons > hide sel cartoons > select coil 515512 atoms, 515133 bonds, 23 pseudobonds, 64312 residues, 63 models selected > show sel cartoons > color (#6.1-61#!4 & sel) gray > select clear > save /Users/sacosta/Desktop/image111.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/sacosta/Desktop/movie8.mp4 Movie saved to /Users/sacosta/Desktop/movie8.mp4 > view orient > movie record > turn y 2 180 > wait 180 > movie encode /Users/sacosta/Desktop/movie8.mp4 Movie saved to /Users/sacosta/Desktop/movie8.mp4 > save /Users/sacosta/Desktop/image112.png supersample 3 > save /Users/sacosta/MICROSCOPY/FERRITIN/NEW-RECONSTRUCTIONS/RELION/relion- > bpa.cxs > close #1 > close #2 > close #3 > open /Users/sacosta/MICROSCOPY/FERRITIN/NEW- > RECONSTRUCTIONS/Particle_4/MD_oct_Particle_4.mrc Opened MD_oct_Particle_4.mrc as #1, grid size 250,250,250, pixel 1.17, shown at level 0.0436, step 1, values float32 > ui tool show ""Map Coordinates"" > open /Users/sacosta/MICROSCOPY/FERRITIN/NEW- > RECONSTRUCTIONS/RELION/BT_P4/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #2, grid size 250,250,250, pixel 1, shown at level 0.0892, step 1, values float32 > select #1 2 models selected > select #2 2 models selected > ~select #2 Nothing selected > select #6 1997994 atoms, 2030202 bonds, 248819 residues, 62 models selected > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models #6,1,0,0,2.0322,0,1,0,2.5047,0,0,1,-0.13049 > view matrix models #6,1,0,0,0.75417,0,1,0,1.2803,0,0,1,-0.074535 > view matrix models #6,1,0,0,0.64123,0,1,0,-0.52001,0,0,1,0.056344 > view matrix models #6,1,0,0,2.0642,0,1,0,0.60256,0,0,1,0.29624 > hide #!6 models > volume #1 level 0.03935 > ui tool show ""Surface Color"" > color sample #1.1 map #2 palette > #ff0000:#ffffff:#0000ff:#808080:#808080:#808080 Map values for surface ""surface"": minimum 0.06623, mean 0.08037, maximum 0.08967 > color sample #1.1 map #2 palette > #ff0000:#ff6666:#ffcccc:#cbcbff:#6565ff:#0000ff Map values for surface ""surface"": minimum 0.06623, mean 0.08037, maximum 0.08967 > movie record > turn y 2 180 > wait 180 > movie encode /Users/sacosta/Desktop/movie9.mp4 Movie saved to /Users/sacosta/Desktop/movie9.mp4 > key red:0.066 #ff6666:0.071 #ffcccc:0.076 #cbcbff:0.080 #6565ff:0.085 > blue:0.090 showTool true > ui mousemode right ""color key"" > ui mousemode right ""translate selected models"" > movie record > turn y 2 180 > wait 180 > movie encode /Users/sacosta/Desktop/movie10.mp4 Movie saved to /Users/sacosta/Desktop/movie10.mp4 > save /Users/sacosta/Desktop/image113.png supersample 3 > volume #1 level 0.03982 > ui mousemode right ""clip rotate"" > color sample #1.1 map #2 palette > 0.06623,#ff0000:0.07092,#ff6666:0.07561,#ffcccc:0.08029,#cbcbff:0.08498,#6565ff:0.08967,#0000ff Map values for surface ""surface"": minimum 0.06665, mean 0.08137, maximum 0.0905 Map values for surface ""cap front"": minimum 0.06669, mean 0.08544, maximum 0.09496 > volume #1 level 0.03274 > ui mousemode right ""clip rotate"" > save /Users/sacosta/Desktop/image114.png supersample 3 > save /Users/sacosta/MICROSCOPY/FERRITIN/NEW-RECONSTRUCTIONS/RELION/relion- > bt_p4.cxs > open /Users/sacosta/MICROSCOPY/FERRITIN/NEW-RECONSTRUCTIONS/RELION/relion- > bpa.cxs Opened MD_Oct_BPA_9Aresolution.mrc as #1, grid size 250,250,250, pixel 0.832, shown at level 0.0287, step 1, values float32 Opened relion_locres.mrc as #2, grid size 250,250,250, pixel 0.832, shown at level 14.3, step 1, values float32 Opened relion_locres_filtered.mrc as #3, grid size 250,250,250, pixel 0.832, shown at level 0.0559, step 1, values float32 opened ChimeraX session ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3rc202111250017 (2021-11-25) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-4.7.101 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1715.60.5.0.0 (iBridge: 19.16.10647.0.0,0) OS Loader Version: 540.60.2~89 Software: System Software Overview: System Version: macOS 12.1 (21C52) Kernel Version: Darwin 21.2.0 Time since boot: 29 days 3:45 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal HP 24w: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: CNC9050NCZ Mirror: Off Online: Yes Rotation: Supported Adapter Type: Apple USB-C Digital AV Adapter Automatically Adjust Brightness: Yes Adapter Firmware Version: 2.35 Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.8 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3rc202111250017 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 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 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 MolecularDynamicsViewer: 1.2 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.7.3 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.2 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.2 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 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 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX