id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9013 QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.5.1-arm64-arm-64bit ChimeraX Version: 1.6.dev202303080949 (2023-03-08 09:49:10 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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""rolloutId"" : ""6297d96be2c9387df974efa4"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""60186475825c62000ccf5450"", ""factorPackIds"" : { }, ""deploymentId"" : 240000026 } ], ""experiments"" : [ { ""treatmentId"" : ""c28e4ee6-1b08-4f90-8e05-2809e78310a3"", ""experimentId"" : ""6317d2003d24842ff850182a"", ""deploymentId"" : 400000013 }, { ""treatmentId"" : ""6dd670af-0633-45e4-ae5f-122ae4df02be"", ""experimentId"" : ""64406ba83deb637ac8a04419"", ""deploymentId"" : 900000005 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6.dev202303080949 (2023-03-08) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/adaina/Documents/PUBLI/FGFR2-InDels-Dana_Farber/2023-follow- > up/SESSION_May5/PREDDIMER/FGFR2_short-1_FGFR2_short-2_best.pdb Chain information for FGFR2_short-1_FGFR2_short-2_best.pdb --- Chain | Description 1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B | No description available > ui tool show Matchmaker > matchmaker #1.7#!1.2-6 to #1.1 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 FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.7), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.137 angstroms; (across all 26 pairs: 0.137) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.102 angstroms; (across all 26 pairs: 0.102) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.3), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.189 angstroms; (across all 26 pairs: 0.189) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.4), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.144 angstroms; (across all 26 pairs: 0.144) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.5), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.133 angstroms; (across all 26 pairs: 0.133) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.6), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.162 angstroms; (across all 26 pairs: 0.162) > matchmaker #1.7#!1.2-6 to #1.1/A pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.7), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.137 angstroms; (across all 26 pairs: 0.137) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.102 angstroms; (across all 26 pairs: 0.102) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.3), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.189 angstroms; (across all 26 pairs: 0.189) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.4), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.144 angstroms; (across all 26 pairs: 0.144) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.5), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.133 angstroms; (across all 26 pairs: 0.133) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.6), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.162 angstroms; (across all 26 pairs: 0.162) > matchmaker #1.7#!1.2-6 to #1.1/A pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.7), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.137 angstroms; (across all 26 pairs: 0.137) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.102 angstroms; (across all 26 pairs: 0.102) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.3), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.189 angstroms; (across all 26 pairs: 0.189) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.4), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.144 angstroms; (across all 26 pairs: 0.144) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.5), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.133 angstroms; (across all 26 pairs: 0.133) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.6), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.162 angstroms; (across all 26 pairs: 0.162) > matchmaker #1.7#!1.2-6 to #1.1/B 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 FGFR2_short-1_FGFR2_short-2_best.pdb, chain B (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.7), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.137 angstroms; (across all 26 pairs: 0.137) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain B (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.102 angstroms; (across all 26 pairs: 0.102) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain B (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.3), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.189 angstroms; (across all 26 pairs: 0.189) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain B (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.4), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.144 angstroms; (across all 26 pairs: 0.144) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain B (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.5), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.133 angstroms; (across all 26 pairs: 0.133) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain B (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.6), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.162 angstroms; (across all 26 pairs: 0.162) No reference and/or match structure/chain chosen > matchmaker #1.2/A to #1.1/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.102 angstroms; (across all 26 pairs: 0.102) > matchmaker #1.7#!1.2-6 to #1.1/A pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.7), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.137 angstroms; (across all 26 pairs: 0.137) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.102 angstroms; (across all 26 pairs: 0.102) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.3), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.189 angstroms; (across all 26 pairs: 0.189) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.4), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.144 angstroms; (across all 26 pairs: 0.144) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.5), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.133 angstroms; (across all 26 pairs: 0.133) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.6), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.162 angstroms; (across all 26 pairs: 0.162) > hide #1.7#!1.2-6 target m > show #1.7#!1.2-6 target m > select H 3122 atoms, 364 residues, 7 models selected > hide sel target a > hide #!1.4 models > hide #!1.5 models > hide #!1.6 models > hide #1.7 models > hide #!1.3 models > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > show #!1.3 models > hide #!1.3 models > show #!1.3 models > hide #!1.3 models > show #!1.4 models > hide #!1.4 models > show #!1.4 models > hide #!1.4 models > show #!1.3 models > show #!1.2 models > hide #!1.3 models > open /Users/adaina/Documents/PUBLI/FGFR2-InDels-Dana_Farber/2023-follow- > up/SESSION_May5/PREDDIMER/F386_A389del_sho-1_F386_A389del_sho-2_best.pdb Chain information for F386_A389del_sho-1_F386_A389del_sho-2_best.pdb --- Chain | Description 2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.1/B 2.2/B 2.3/B 2.4/B 2.5/B 2.6/B 2.7/B | No description available > show #!1.3 models > hide #!1.3 models > select H 5740 atoms, 672 residues, 14 models selected > hide (#2.7#!1.1-2#!2.1-6 & sel) target a > ui tool show Matchmaker > matchmaker #1.7#2.7#!1.2-6#!2.1-6 to #1.1/A pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.7), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.137 angstroms; (across all 26 pairs: 0.137) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.7), sequence alignment score = 96.4 RMSD between 10 pruned atom pairs is 0.112 angstroms; (across all 22 pairs: 4.308) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.102 angstroms; (across all 26 pairs: 0.102) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.3), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.189 angstroms; (across all 26 pairs: 0.189) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.4), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.144 angstroms; (across all 26 pairs: 0.144) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.5), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.133 angstroms; (across all 26 pairs: 0.133) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.6), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.162 angstroms; (across all 26 pairs: 0.162) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.1), sequence alignment score = 96.4 RMSD between 10 pruned atom pairs is 0.070 angstroms; (across all 22 pairs: 4.303) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.2), sequence alignment score = 96.4 RMSD between 10 pruned atom pairs is 0.125 angstroms; (across all 22 pairs: 4.313) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.3), sequence alignment score = 96.4 RMSD between 10 pruned atom pairs is 0.172 angstroms; (across all 22 pairs: 4.320) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.4), sequence alignment score = 90.4 RMSD between 11 pruned atom pairs is 0.204 angstroms; (across all 22 pairs: 4.310) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.5), sequence alignment score = 96.4 RMSD between 10 pruned atom pairs is 0.101 angstroms; (across all 22 pairs: 4.316) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.6), sequence alignment score = 96.4 RMSD between 10 pruned atom pairs is 0.115 angstroms; (across all 22 pairs: 4.327) > hide #!2.1 models > hide #!2.2 models > hide #!2.3 models > hide #!2.4 models > hide #!2.5 models > hide #!2.6 models > hide #2.7 models > show #!2.2 models > show #!2.1 models > hide #!2.2 models > hide #!2.1 models > show #!2.2 models > hide #!2.2 models > show #!2.3 models > hide #!1.2 models > show #!2.1 models > hide #!2.3 models > show #!2.2 models > hide #!2.1 models > hide #!2.2 models > show #!2.3 models > show #!2.4 models > hide #!2.3 models > show #!2.5 models > hide #!2.4 models > hide #!2.5 models > show #!2.6 models > hide #!2.6 models > show #2.7 models > hide #2.7 models > show #!2.1 models > show #!2.2 models > hide #!2.1 models > hide #!2.2 models > ui tool show Matchmaker > matchmaker #1.7#2.7#!1.2-6#!2.1-6 to #1.1 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 FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.7), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.137 angstroms; (across all 26 pairs: 0.137) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.7), sequence alignment score = 96.4 RMSD between 10 pruned atom pairs is 0.112 angstroms; (across all 22 pairs: 4.308) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.102 angstroms; (across all 26 pairs: 0.102) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.3), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.189 angstroms; (across all 26 pairs: 0.189) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.4), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.144 angstroms; (across all 26 pairs: 0.144) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.5), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.133 angstroms; (across all 26 pairs: 0.133) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.6), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.162 angstroms; (across all 26 pairs: 0.162) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.1), sequence alignment score = 96.4 RMSD between 10 pruned atom pairs is 0.070 angstroms; (across all 22 pairs: 4.303) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.2), sequence alignment score = 96.4 RMSD between 10 pruned atom pairs is 0.125 angstroms; (across all 22 pairs: 4.313) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.3), sequence alignment score = 96.4 RMSD between 10 pruned atom pairs is 0.172 angstroms; (across all 22 pairs: 4.320) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.4), sequence alignment score = 90.4 RMSD between 11 pruned atom pairs is 0.204 angstroms; (across all 22 pairs: 4.310) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.5), sequence alignment score = 96.4 RMSD between 10 pruned atom pairs is 0.101 angstroms; (across all 22 pairs: 4.316) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.6), sequence alignment score = 96.4 RMSD between 10 pruned atom pairs is 0.115 angstroms; (across all 22 pairs: 4.327) > show #!2.1 models > show #!2.2 models > show #!2.3 models > hide #!2.1 models > hide #!2.2 models > hide #!2.3 models > show #!2.1 models > show #!2.2 models > hide #!2.1 models > show #!2.3 models > hide #!2.2 models > show #!2.4 models > hide #!2.3 models > show #!2.5 models > hide #!2.4 models > show #!2.6 models > hide #!2.5 models > hide #!2.6 models > show #2.7 models > hide #2.7 models > show #2.7 models > hide #2.7 models > ui tool show Matchmaker > matchmaker #1.7#!1.1,3-6#!2.1-6 to #1.2 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 FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.7), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.120 angstroms; (across all 26 pairs: 0.120) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.1), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.102 angstroms; (across all 26 pairs: 0.102) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.3), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.178 angstroms; (across all 26 pairs: 0.178) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.4), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.142 angstroms; (across all 26 pairs: 0.142) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.5), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.111 angstroms; (across all 26 pairs: 0.111) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2) with FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.6), sequence alignment score = 138.2 RMSD between 26 pruned atom pairs is 0.163 angstroms; (across all 26 pairs: 0.163) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.1), sequence alignment score = 96.4 RMSD between 10 pruned atom pairs is 0.157 angstroms; (across all 22 pairs: 4.315) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.2), sequence alignment score = 96.4 RMSD between 10 pruned atom pairs is 0.166 angstroms; (across all 22 pairs: 4.321) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.3), sequence alignment score = 96.4 RMSD between 10 pruned atom pairs is 0.172 angstroms; (across all 22 pairs: 4.335) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.4), sequence alignment score = 90.4 RMSD between 11 pruned atom pairs is 0.226 angstroms; (across all 22 pairs: 4.323) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.5), sequence alignment score = 96.4 RMSD between 10 pruned atom pairs is 0.130 angstroms; (across all 22 pairs: 4.323) Matchmaker FGFR2_short-1_FGFR2_short-2_best.pdb, chain A (#1.2) with F386_A389del_sho-1_F386_A389del_sho-2_best.pdb, chain A (#2.6), sequence alignment score = 96.4 RMSD between 10 pruned atom pairs is 0.160 angstroms; (across all 22 pairs: 4.335) > show #!2.1 models > show #!1.2 models > hide #!1.1 models > show #!2.2 models > hide #!2.1 models > hide #!2.2 models > show #!2.3 models > hide #!2.3 models > show #!2.4 models > show #!2.5 models > hide #!2.4 models > select #1.2/A:12 20 atoms, 19 bonds, 1 pseudobond, 2 residues, 2 models selected > select #1.2/A:13 19 atoms, 17 bonds, 1 pseudobond, 2 residues, 2 models selected > hide #!2.5 models > select add #1.2/A:12 39 atoms, 36 bonds, 2 pseudobonds, 4 residues, 2 models selected > select add #1.2/A:14 58 atoms, 53 bonds, 3 pseudobonds, 6 residues, 2 models selected > select add #1.2/A:15 68 atoms, 61 bonds, 4 pseudobonds, 8 residues, 2 models selected > select up 201 atoms, 198 bonds, 4 pseudobonds, 26 residues, 2 models selected > select up 403 atoms, 401 bonds, 4 pseudobonds, 52 residues, 2 models selected > select up 426 atoms, 401 bonds, 4 pseudobonds, 52 residues, 2 models selected > select up 852 atoms, 802 bonds, 56 pseudobonds, 104 residues, 2 models selected > set bgColor white > ui tool show ""Color Actions"" > color sel orange > color sel salmon > color sel dark salmon > color sel salmon > color sel light salmon > color sel dark salmon > select clear > select #1.2/A:12 20 atoms, 19 bonds, 1 pseudobond, 2 residues, 2 models selected > select add #1.2/A:13 39 atoms, 36 bonds, 2 pseudobonds, 4 residues, 2 models selected > select add #1.2/A:14 58 atoms, 53 bonds, 3 pseudobonds, 6 residues, 2 models selected > select add #1.2/A:15 68 atoms, 61 bonds, 4 pseudobonds, 8 residues, 2 models selected > select add #1.2/B:38 88 atoms, 80 bonds, 5 pseudobonds, 10 residues, 2 models selected > select add #1.2/B:39 107 atoms, 97 bonds, 6 pseudobonds, 12 residues, 2 models selected > select add #1.2/B:40 126 atoms, 114 bonds, 7 pseudobonds, 14 residues, 2 models selected > select add #1.2/B:41 136 atoms, 122 bonds, 8 pseudobonds, 16 residues, 2 models selected > color (#!1.2 & sel) orange > show #!2.6 models > hide #!2.6 models > show #!2.5 models > select clear > color #1.2#2.5#!1-2 byhetero > hide #!2.5 models > show #!2.4 models > hide #!2.4 models > show #!2.5 models > hide #!2.5 models > show #!2.6 models > hide #!2.6 models > show #2.7 models > hide #2.7 models > show #!2.5 models > save /Users/adaina/Desktop/image16.png supersample 3 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.dev202303080949 (2023-03-08) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,1 Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 7459.141.1 OS Loader Version: 7459.141.1 Software: System Software Overview: System Version: macOS 12.5.1 (21G83) Kernel Version: Darwin 21.6.0 Time since boot: 54 days 4:12 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL S2721DS: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 75.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9 ChimeraX-AddH: 2.2.3 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.9 ChimeraX-AtomicLibrary: 10.0.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 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: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.dev202303080949 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.3.3 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.11 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.8 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7 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-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 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: 1.10.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.2 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.2 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.6 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.0.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.4 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.2.0 jupyterlab-widgets: 3.0.5 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 pandas: 1.5.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.1.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.2 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.2 python-dateutil: 2.8.2 pytz: 2022.7.1 pyzmq: 25.0.0 qtconsole: 5.4.0 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.0.2 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.9.0 typing-extensions: 4.5.0 urllib3: 1.26.14 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.5 zipp: 3.15.0 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX