id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17432 Crash moving window between screens bicoid@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. 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""928dfbce-0cc0-4f29-866f-5542e51ad72e"", ""experimentId"" : ""67f46e2984eaf455d73c609a"", ""deploymentId"" : 400000001 } ] } } Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/npd1/Desktop/CasXMax paper/Figure models/K610c.cxs"" Log from Fri Dec 20 14:41:34 2024UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/npd1/Desktop/R610b.cxs format session Log from Thu Dec 19 14:32:51 2024UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/npd1/Desktop/R610a.cxs format session Log from Thu Dec 19 09:27:48 2024UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/npd1/Desktop/R610.cxs Log from Thu Dec 19 08:48:26 2024UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/npd1/Desktop/R610.cxs Log from Thu Dec 19 08:17:31 2024UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/npd1/Desktop/K610.cxs Log from Thu Dec 19 08:04:12 2024UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/npd1/Desktop/T26a.cxs Log from Wed Dec 18 18:16:40 2024UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/npd1/Desktop/T26.cxs format session Log from Wed Dec 18 17:53:52 2024UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/npd1/Desktop/Session 3a surfaces.cxs"" Log from Tue Dec 17 16:34:16 2024UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/npd1/Desktop/Session 2.cxs"" Log from Tue Dec 17 15:14:27 2024UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/npd1/Desktop/CasX & CasY AF modeling/X2+X2MAX stateI & state > II.cxs"" Log from Thu Nov 14 19:14:01 2024 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/npd1/Downloads/X2-Max 7WAY (state I).pdb"" X2-Max 7WAY (state I).pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more info...] Chain information for X2-Max 7WAY (state I).pdb #1 --- Chain | Description D | No description available > open ""/Users/npd1/Downloads/X2-Max 7WB0 (state III).pdb"" X2-Max 7WB0 (state III).pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more info...] Chain information for X2-Max 7WB0 (state III).pdb #2 --- Chain | Description D | No description available > open ""/Users/npd1/Downloads/X2-Max 7WAZ (state II).pdb"" X2-Max 7WAZ (state II).pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more info...] Chain information for X2-Max 7WAZ (state II).pdb #3 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #2-3 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 X2-Max 7WAY (state I).pdb, chain D (#1) with X2-Max 7WB0 (state III).pdb, chain D (#2), sequence alignment score = 4510.1 RMSD between 597 pruned atom pairs is 0.734 angstroms; (across all 975 pairs: 15.887) Matchmaker X2-Max 7WAY (state I).pdb, chain D (#1) with X2-Max 7WAZ (state II).pdb, chain A (#3), sequence alignment score = 4935.5 RMSD between 656 pruned atom pairs is 0.994 angstroms; (across all 975 pairs: 4.408) > select /D:26,610,808 66 atoms, 60 bonds, 6 residues, 2 models selected > show sel atoms > select /D:26,610,808 66 atoms, 60 bonds, 6 residues, 2 models selected > color sel red > hide #1 models > hide #2 models > show #2 models > hide #2 models > show #2 models > show #1 models > hide #2 models > show #2 models > hide #3 models > hide #2 models > hide #1 models > show #3 models > select add #3 7987 atoms, 8141 bonds, 981 residues, 3 models selected > select add #2 15875 atoms, 16192 bonds, 1953 residues, 3 models selected > select add #1 23763 atoms, 24243 bonds, 2925 residues, 3 models selected > select subtract #1 15842 atoms, 16162 bonds, 1950 residues, 2 models selected > select subtract #2 7921 atoms, 8081 bonds, 975 residues, 1 model selected > select /D:26,610,808 66 atoms, 60 bonds, 6 residues, 2 models selected > select /A:26,610,808 33 atoms, 30 bonds, 3 residues, 1 model selected > show sel atoms > color sel red > show #1 models > show #2 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select clear > open ""/Users/npd1/Library/CloudStorage/Dropbox/Alphafold/Structures/CasX2 > (cryoEM)/7way (CasX2 state I).pdb"" 7way (CasX2 state I).pdb title: Plmcasx-SGRNAV1-dsDNA ternary complex At NTS loading state [more info...] Chain information for 7way (CasX2 state I).pdb #4 --- Chain | Description A | dplmcasx B | DNA (33-mer) C | DNA (27-mer) D | RNA > open ""/Users/npd1/Library/CloudStorage/Dropbox/Alphafold/Structures/CasX2 > (cryoEM)/7way (CasX2 state I).pdb"" 7way (CasX2 state I).pdb title: Plmcasx-SGRNAV1-dsDNA ternary complex At NTS loading state [more info...] Chain information for 7way (CasX2 state I).pdb #5 --- Chain | Description A | dplmcasx B | DNA (33-mer) C | DNA (27-mer) D | RNA The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open ""/Users/npd1/Library/CloudStorage/Dropbox/Alphafold/Structures/CasX2 > (cryoEM)/7waz (CasX2 state II.cif"" 7waz (CasX2 state II.cif title: PlmCasX-sgRNAv1-dsDNA ternary complex at ts loading state [more info...] Chain information for 7waz (CasX2 state II.cif #6 --- Chain | Description | UniProt A | dPlmCasX | A0A1G3BXR9_9BACT 1-978 B | TS-DNA | C | NTS-DNA | D | RNA (115-MER) | > open ""/Users/npd1/Library/CloudStorage/Dropbox/Alphafold/Structures/CasX2 > (cryoEM)/7wb0 (CasX2 state III).cif"" 7wb0 (CasX2 state III).cif title: PlmCasX-sgRNAv1-dsDNA ternary complex at nts loading state with flexible H2 domain [more info...] Chain information for 7wb0 (CasX2 state III).cif #7 --- Chain | Description | UniProt A | dPlmCasX | A0A1G3BXR9_9BACT 1-978 B | TS-DNA | C | NTS-DNA | D | RNA (115-MER) | > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > matchmaker #1-3#!4,6-7 to #5 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 7way (CasX2 state I).pdb, chain A (#5) with X2-Max 7WAY (state I).pdb, chain D (#1), sequence alignment score = 5017.3 RMSD between 960 pruned atom pairs is 0.065 angstroms; (across all 960 pairs: 0.065) Matchmaker 7way (CasX2 state I).pdb, chain A (#5) with X2-Max 7WB0 (state III).pdb, chain D (#2), sequence alignment score = 4468.3 RMSD between 593 pruned atom pairs is 0.731 angstroms; (across all 960 pairs: 15.989) Matchmaker 7way (CasX2 state I).pdb, chain A (#5) with X2-Max 7WAZ (state II).pdb, chain A (#3), sequence alignment score = 4885.9 RMSD between 652 pruned atom pairs is 0.994 angstroms; (across all 960 pairs: 4.406) Matchmaker 7way (CasX2 state I).pdb, chain A (#5) with 7way (CasX2 state I).pdb, chain A (#4), sequence alignment score = 5089.5 RMSD between 960 pruned atom pairs is 0.000 angstroms; (across all 960 pairs: 0.000) Matchmaker 7way (CasX2 state I).pdb, chain A (#5) with 7waz (CasX2 state II.cif, chain A (#6), sequence alignment score = 4878.9 RMSD between 649 pruned atom pairs is 1.008 angstroms; (across all 952 pairs: 4.384) Matchmaker 7way (CasX2 state I).pdb, chain A (#5) with 7wb0 (CasX2 state III).cif, chain A (#7), sequence alignment score = 4690.5 RMSD between 592 pruned atom pairs is 0.737 angstroms; (across all 797 pairs: 3.068) > hide #!5 models > hide #!6 models > hide #!7 models > sequence chain #4/B Alignment identifier is 4/B The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > nucleotides #1-3#!4 fill > style nucleic & #1-3#!4 stick Changed 3667 atom styles > color #1-4 white > undo > select #7/B:-2-30 674 atoms, 753 bonds, 33 residues, 1 model selected > select #7/B:-2-30 674 atoms, 753 bonds, 33 residues, 1 model selected > select #7/B:-2-30 674 atoms, 753 bonds, 33 residues, 1 model selected > select #7/B:-2-30 674 atoms, 753 bonds, 33 residues, 1 model selected > nucleotides #1-3#!4 fill > style nucleic & #1-3#!4 stick Changed 3667 atom styles > color #1-4 light gray > undo > color #4 #517a53ff > color #4 #2851e4ff > select add #4 12127 atoms, 12794 bonds, 3 pseudobonds, 1168 residues, 3 models selected > select add #7 21549 atoms, 22694 bonds, 165 pseudobonds, 2107 residues, 5 models selected > select subtract #7 11453 atoms, 12041 bonds, 3 pseudobonds, 1135 residues, 2 models selected > select subtract #4 Nothing selected > select add #4 11453 atoms, 12041 bonds, 3 pseudobonds, 1135 residues, 2 models selected > color #3 #fb001dff > color #2 #1bce0eff > color #3 #1bce0eff > color #1 #1bce0eff > select clear > select /A:26,610,808 133 atoms, 118 bonds, 15 residues, 5 models selected > show sel & #3#!4 atoms > color (#3#!4 & sel) red > select /D:26,610,808 158 atoms, 160 bonds, 10 residues, 6 models selected > color (#1-2#!4 & sel) red > select #4/D:26 23 atoms, 25 bonds, 1 residue, 1 model selected > color sel blue > select #6/D:1-122 2446 atoms, 2734 bonds, 78 pseudobonds, 115 residues, 3 models selected > select #6/D:1-122 2446 atoms, 2734 bonds, 78 pseudobonds, 115 residues, 3 models selected > select #6/C:1-12 245 atoms, 273 bonds, 12 residues, 1 model selected > select #6/B:1-30 614 atoms, 686 bonds, 30 residues, 1 model selected > select #4/D:1-122 2446 atoms, 2734 bonds, 1 pseudobond, 115 residues, 2 models selected > select #4/C:1-27 547 atoms, 611 bonds, 27 residues, 1 model selected > select #4/B:-2-30 674 atoms, 753 bonds, 33 residues, 1 model selected > show sel atoms [Repeated 1 time(s)] > hide sel cartoons > select #1/D:26@NH2 1 atom, 1 residue, 1 model selected > select add #4/C:11@O2 2 atoms, 2 residues, 2 models selected > ui tool show H-Bonds The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui tool show Distances > distance #1/D:26@NH2 #4/C:11@O2 Distance between X2-Max 7WAY (state I).pdb #1/D ARG 26 NH2 and 7way (CasX2 state I).pdb #4/C DT 11 O2: 4.427Å > select #4/A:610@NZ 1 atom, 1 residue, 1 model selected > select add #4/B:22@OP1 2 atoms, 2 residues, 1 model selected > distance #4/A:610@NZ #4/B:22@OP1 Distance between 7way (CasX2 state I).pdb #4/A LYS 610 NZ and /B DG 22 OP1: 4.707Å > select #4/C:25 19 atoms, 20 bonds, 1 residue, 1 model selected > select #4/D 2446 atoms, 2734 bonds, 1 pseudobond, 115 residues, 2 models selected > color (#!4 & sel) light gray > color (#!4 & sel) cornflower blue > select #3/B Nothing selected > select #4/B 674 atoms, 753 bonds, 33 residues, 1 model selected > color sel light gray > select #4/C 547 atoms, 611 bonds, 27 residues, 1 model selected > show sel atoms > show sel cartoons > hide sel cartoons > nucleotides sel fill > style nucleic & sel stick Changed 547 atom styles > color sel gray > select clear > select #1/D:26@NH2 1 atom, 1 residue, 1 model selected > select #4/B:20@OP1 1 atom, 1 residue, 1 model selected > select add #1/D:26@NH2 2 atoms, 2 residues, 2 models selected > distance #4/B:20@OP1 #1/D:26@NH2 Distance between 7way (CasX2 state I).pdb #4/B DA 20 OP1 and X2-Max 7WAY (state I).pdb #1/D ARG 26 NH2: 6.506Å > select #1/D:26@NH2 1 atom, 1 residue, 1 model selected > select add #4/B:21@OP1 2 atoms, 2 residues, 2 models selected > distance #1/D:26@NH2 #4/B:21@OP1 Distance between X2-Max 7WAY (state I).pdb #1/D ARG 26 NH2 and 7way (CasX2 state I).pdb #4/B DT 21 OP1: 5.251Å > select #4/D 2446 atoms, 2734 bonds, 1 pseudobond, 115 residues, 2 models selected > hide sel cartoons > select #1/D:26@NH2 1 atom, 1 residue, 1 model selected > select add #3/A:26@NH2 2 atoms, 2 residues, 2 models selected > distance #1/D:26@NH2 #3/A:26@NH2 Distance between X2-Max 7WAY (state I).pdb #1/D ARG 26 NH2 and X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2: 1.454Å > select #3/A:26@NH2 1 atom, 1 residue, 1 model selected > select #3/A:26@NH2 1 atom, 1 residue, 1 model selected > select add #4/B:21@OP1 2 atoms, 2 residues, 2 models selected > distance #3/A:26@NH2 #4/B:21@OP1 Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2 and 7way (CasX2 state I).pdb #4/B DT 21 OP1: 4.148Å > select #3/A:26@NH2 1 atom, 1 residue, 1 model selected > select add #4/B:20@OP1 2 atoms, 2 residues, 2 models selected > distance #3/A:26@NH2 #4/B:20@OP1 Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2 and 7way (CasX2 state I).pdb #4/B DA 20 OP1: 5.079Å > select #3/A:26@NH2 1 atom, 1 residue, 1 model selected > select add #4/B:20@OP2 2 atoms, 2 residues, 2 models selected > distance #3/A:26@NH2 #4/B:20@OP2 Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2 and 7way (CasX2 state I).pdb #4/B DA 20 OP2: 5.657Å > hide #3 models > show #3 models > hide #2 models > select #3/A:26@NH2 1 atom, 1 residue, 1 model selected > select add #4/C:11@O2 2 atoms, 2 residues, 2 models selected > distance #3/A:26@NH2 #4/C:11@O2 Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2 and 7way (CasX2 state I).pdb #4/C DT 11 O2: 4.483Å > select #1/D:26@NH2 1 atom, 1 residue, 1 model selected > select add #4/B:21@OP2 2 atoms, 2 residues, 2 models selected > distance #1/D:26@NH2 #4/B:21@OP2 Distance between X2-Max 7WAY (state I).pdb #1/D ARG 26 NH2 and 7way (CasX2 state I).pdb #4/B DT 21 OP2: 5.750Å > select #3/A:26@NH2 1 atom, 1 residue, 1 model selected > select add #4/B:21@OP2 2 atoms, 2 residues, 2 models selected > distance #3/A:26@NH2 #4/B:21@OP2 Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2 and 7way (CasX2 state I).pdb #4/B DT 21 OP2: 5.141Å > select #1/D:26@NH2 1 atom, 1 residue, 1 model selected > select add #4/B:20@OP2 2 atoms, 2 residues, 2 models selected > distance #1/D:26@NH2 #4/B:20@OP2 Distance between X2-Max 7WAY (state I).pdb #1/D ARG 26 NH2 and 7way (CasX2 state I).pdb #4/B DA 20 OP2: 7.074Å > hide #3 models > show #3 models > hide #1 models > show #1 models > select #3/A:610@NH1 1 atom, 1 residue, 1 model selected > select add #4/B:22@OP1 2 atoms, 2 residues, 2 models selected > distance #3/A:610@NH1 #4/B:22@OP1 Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 610 NH1 and 7way (CasX2 state I).pdb #4/B DG 22 OP1: 7.736Å > select #1/D:610@NH1 1 atom, 1 residue, 1 model selected > select add #4/B:22@OP1 2 atoms, 2 residues, 2 models selected > distance #1/D:610@NH1 #4/B:22@OP1 Distance between X2-Max 7WAY (state I).pdb #1/D ARG 610 NH1 and 7way (CasX2 state I).pdb #4/B DG 22 OP1: 8.474Å > select #4/A:610@NZ 1 atom, 1 residue, 1 model selected > select add #4/B:21@OP2 2 atoms, 2 residues, 1 model selected > distance #4/A:610@NZ #4/B:21@OP2 Distance between 7way (CasX2 state I).pdb #4/A LYS 610 NZ and /B DT 21 OP2: 4.599Å > hide #!4 models > show #!4 models > hide #4.1 models > show #4.1 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hbonds sel reveal true Atom specifier selects no atoms > hide #3 models > hide #1 models > select #4/B:7-10 79 atoms, 86 bonds, 4 residues, 1 model selected > select #4/C:8-11 80 atoms, 88 bonds, 4 residues, 1 model selected > color sel orange > select clear > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > select #1/D:610@NH1 1 atom, 1 residue, 1 model selected > select add #4/B:21@OP2 2 atoms, 2 residues, 2 models selected > distance #1/D:610@NH1 #4/B:21@OP2 Distance between X2-Max 7WAY (state I).pdb #1/D ARG 610 NH1 and 7way (CasX2 state I).pdb #4/B DT 21 OP2: 8.981Å > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #!4 models > show #!4 models > hide #1 models > show #1 models > hide #!4 models > show #2 models > hide #1 models > hide #2 models > show #!4 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!4 models > show #2 models > hide #2 models > show #2 models > select #2/A:26,610,808 Nothing selected > select #2/D:26,610,808 33 atoms, 30 bonds, 3 residues, 1 model selected > select #6/A:26,610,808 25 atoms, 22 bonds, 3 residues, 1 model selected > show sel atoms > color sel lime > color #2 #c1d228ff > select #6/B,C,D 3305 atoms, 3693 bonds, 130 pseudobonds, 157 residues, 3 models selected > show sel atoms > nucleotides sel fill > style nucleic & sel stick Changed 3305 atom styles > hide sel cartoons > select #6/B 614 atoms, 686 bonds, 30 residues, 1 model selected > color sel light gray > select #6/C 245 atoms, 273 bonds, 12 residues, 1 model selected > color sel dim gray > select #6/D 2446 atoms, 2734 bonds, 78 pseudobonds, 115 residues, 3 models selected > color (#!6 & sel) blue > select #2/D 7921 atoms, 8081 bonds, 975 residues, 1 model selected > select #2/D:26,610,808 33 atoms, 30 bonds, 3 residues, 1 model selected > color sel red > select #2/D:610@NH1 1 atom, 1 residue, 1 model selected > select add #6/B:22@OP1 2 atoms, 2 residues, 2 models selected > distance #2/D:610@NH1 #6/B:22@OP1 Distance between X2-Max 7WB0 (state III).pdb #2/D ARG 610 NH1 and 7waz (CasX2 state II.cif #6/B DG 22 OP1: 7.671Å > select add #6/A:610@NZ 3 atoms, 3 residues, 2 models selected > select #6/A:610@NZ 1 atom, 1 residue, 1 model selected > select add #2/D:610@NH1 2 atoms, 2 residues, 2 models selected > distance #6/A:610@NZ #2/D:610@NH1 Distance between 7waz (CasX2 state II.cif #6/A LYS 610 NZ and X2-Max 7WB0 (state III).pdb #2/D ARG 610 NH1: 4.628Å > select subtract #6/A:610@NZ 1 atom, 1 residue, 1 model selected > select #6/A:610@NZ 1 atom, 1 residue, 1 model selected > select add #6/B:22@OP1 2 atoms, 2 residues, 1 model selected > distance #6/A:610@NZ #6/B:22@OP1 Distance between 7waz (CasX2 state II.cif #6/A LYS 610 NZ and /B DG 22 OP1: 6.773Å > select #6/A:610@NZ 1 atom, 1 residue, 1 model selected > select add #6/B:21@OP2 2 atoms, 2 residues, 1 model selected > distance #6/A:610@NZ #6/B:21@OP2 Distance between 7waz (CasX2 state II.cif #6/A LYS 610 NZ and /B DT 21 OP2: 4.311Å > select add #2/D:610@NH1 3 atoms, 3 residues, 2 models selected > select #2/D:610@NH1 1 atom, 1 residue, 1 model selected > select add #6/B:21@OP2 2 atoms, 2 residues, 2 models selected > distance #2/D:610@NH1 #6/B:21@OP2 Distance between X2-Max 7WB0 (state III).pdb #2/D ARG 610 NH1 and 7waz (CasX2 state II.cif #6/B DT 21 OP2: 8.703Å > select #2/D:26@NH2 1 atom, 1 residue, 1 model selected > select #6/B:21@OP1 1 atom, 1 residue, 1 model selected > select add #2/D:26@NH2 2 atoms, 2 residues, 2 models selected > distance #6/B:21@OP1 #2/D:26@NH2 Distance between 7waz (CasX2 state II.cif #6/B DT 21 OP1 and X2-Max 7WB0 (state III).pdb #2/D ARG 26 NH2: 4.733Å Drag select of 3 residues, 6 atoms, 5 bonds, 3 shapes > select #6/B:20@OP1 1 atom, 1 residue, 1 model selected > select add #2/D:26@NH2 2 atoms, 2 residues, 2 models selected > distance #6/B:20@OP1 #2/D:26@NH2 Distance between 7waz (CasX2 state II.cif #6/B DA 20 OP1 and X2-Max 7WB0 (state III).pdb #2/D ARG 26 NH2: 4.695Å > select #2/D:26@NH2 1 atom, 1 residue, 1 model selected > select #2/D:26@NH2 1 atom, 1 residue, 1 model selected > select add #6/C:12@O2 2 atoms, 2 residues, 2 models selected > distance #2/D:26@NH2 #6/C:12@O2 Distance between X2-Max 7WB0 (state III).pdb #2/D ARG 26 NH2 and 7waz (CasX2 state II.cif #6/C DC 12 O2: 4.743Å > select #2/D:26@NH2 1 atom, 1 residue, 1 model selected > select add #6/B:21@OP2 2 atoms, 2 residues, 2 models selected > distance #2/D:26@NH2 #6/B:21@OP2 Distance between X2-Max 7WB0 (state III).pdb #2/D ARG 26 NH2 and 7waz (CasX2 state II.cif #6/B DT 21 OP2: 6.180Å > hide #!6 models > show #1 models > select #1/D:26@NH2 1 atom, 1 residue, 1 model selected > select add #2/D:26@NH2 2 atoms, 2 residues, 2 models selected > distance #1/D:26@NH2 #2/D:26@NH2 Distance between X2-Max 7WAY (state I).pdb #1/D ARG 26 NH2 and X2-Max 7WB0 (state III).pdb #2/D ARG 26 NH2: 0.743Å > hide #1 models > show #!6 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > select #6/C:9-12 79 atoms, 87 bonds, 4 residues, 1 model selected > color sel orange > show #!5 models > hide #2 models > hide #!6 models > show #!6 models > hide #!5 models > show #!4 models > hide #!6 models > select #4/C:7-10 80 atoms, 88 bonds, 4 residues, 1 model selected > color sel orange > select #4/C:11 20 atoms, 21 bonds, 1 residue, 1 model selected > color sel blue > show #!6 models > hide #!6 models > show #!5 models > hide #!5 models > show #!6 models > select #6/C:11 20 atoms, 21 bonds, 1 residue, 1 model selected > color sel medium blue > select #6/C:7-10 80 atoms, 88 bonds, 4 residues, 1 model selected > color sel orange > hide #!6 models > show #1 models > hide #1 models > show #3 models > hide #!4 models > show #!6 models > select #3/A:26@NH2 1 atom, 1 residue, 1 model selected > select add #6/B:21@OP1 2 atoms, 2 residues, 2 models selected > distance #3/A:26@NH2 #6/B:21@OP1 Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2 and 7waz (CasX2 state II.cif #6/B DT 21 OP1: 4.033Å > select #3/A:26@NH1 1 atom, 1 residue, 1 model selected > select add #6/B:21@OP1 2 atoms, 2 residues, 2 models selected > distance #3/A:26@NH1 #6/B:21@OP1 Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH1 and 7waz (CasX2 state II.cif #6/B DT 21 OP1: 4.895Å > select clear Drag select of 1 atoms > select add #6/C:12@O2 2 atoms, 2 residues, 2 models selected > distance #3/A:26@NH2 #6/C:12@O2 Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2 and 7waz (CasX2 state II.cif #6/C DC 12 O2: 4.603Å > select #3/A:440 9 atoms, 8 bonds, 1 residue, 1 model selected > select #6/B:19@O3' 1 atom, 1 residue, 1 model selected > select #6/B:20@OP1 1 atom, 1 residue, 1 model selected Exactly two atoms must be selected! > select #3/A:26@NH2 1 atom, 1 residue, 1 model selected > select add #6/B:20@OP1 2 atoms, 2 residues, 2 models selected > distance #3/A:26@NH2 #6/B:20@OP1 Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2 and 7waz (CasX2 state II.cif #6/B DA 20 OP1: 3.853Å > select #6/C:11 20 atoms, 21 bonds, 1 residue, 1 model selected > select #6/C:12 19 atoms, 20 bonds, 1 residue, 1 model selected > color sel medium blue > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #!4 models > hide #!4 models > show #!4 models > hide #!6 models > hide #3 models > show #3 models > show #!5 models > hide #!5 models > hide #3 models > hide #!4 models > show #!4 models > show #!6 models > hide #!4 models > show #3 models > show #1 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!6 models > hide #!5 models > hide #3 models > hide #1 models > show #!4 models > show #!6 models > select /C 1886 atoms, 2106 bonds, 93 residues, 4 models selected > select #4/C:1-27 547 atoms, 611 bonds, 27 residues, 1 model selected > select #6/B:1-30 614 atoms, 686 bonds, 30 residues, 1 model selected > select #6/C:1-12 245 atoms, 273 bonds, 12 residues, 1 model selected > hide #!4 models > show #2 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #2 models > show #!4 models > hide #!6 models > hide #!4 models > show #3 models > hide #1 models > show #!6 models > select #3/A:26@NH2 1 atom, 1 residue, 1 model selected > select add #6/C:11@O2 2 atoms, 2 residues, 2 models selected > distance #3/A:26@NH2 #6/C:11@O2 Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2 and 7waz (CasX2 state II.cif #6/C DT 11 O2: 8.318Å > hide #3 models > show #3 models > hide #3 models > show #1 models > hide #!6 models > show #!4 models > select #1/D:26@NH2 1 atom, 1 residue, 1 model selected > select add #4/C:12@O2 2 atoms, 2 residues, 2 models selected > distance #1/D:26@NH2 #4/C:12@O2 Distance between X2-Max 7WAY (state I).pdb #1/D ARG 26 NH2 and 7way (CasX2 state I).pdb #4/C DC 12 O2: 7.267Å > hide #!4 models > hide #1 models > show #1 models > show #!4 models > hide #1 models > show #3 models > hide #!4 models > show #!6 models > hide #!6 models > show #!4 models > hide #3 models > show #1 models > select #4/C:21@OP2 1 atom, 1 residue, 1 model selected > select add #1/D:808@NH1 2 atoms, 2 residues, 2 models selected > distance #4/C:21@OP2 #1/D:808@NH1 Distance between 7way (CasX2 state I).pdb #4/C DT 21 OP2 and X2-Max 7WAY (state I).pdb #1/D ARG 808 NH1: 0.876Å > select #1/D:808@NH2 1 atom, 1 residue, 1 model selected > select add #4/C:21@OP2 2 atoms, 2 residues, 2 models selected > distance #1/D:808@NH2 #4/C:21@OP2 Distance between X2-Max 7WAY (state I).pdb #1/D ARG 808 NH2 and 7way (CasX2 state I).pdb #4/C DT 21 OP2: 2.158Å > select #4/A:808@NZ 1 atom, 1 residue, 1 model selected > select add #4/C:21@OP2 2 atoms, 2 residues, 1 model selected > distance #4/A:808@NZ #4/C:21@OP2 Distance between 7way (CasX2 state I).pdb #4/A LYS 808 NZ and /C DT 21 OP2: 3.776Å > show #3 models > hide #1 models > hide #!4 models > show #!6 models > select #6/A:808@NZ 1 atom, 1 residue, 1 model selected > select add #6/B:3@OP1 2 atoms, 2 residues, 1 model selected > distance #6/A:808@NZ #6/B:3@OP1 Distance between 7waz (CasX2 state II.cif #6/A LYS 808 NZ and /B DT 3 OP1: 2.855Å > select add #3/A:808@NH2 3 atoms, 3 residues, 2 models selected > select #3/A:808@NH2 1 atom, 1 residue, 1 model selected > select add #6/B:3@OP1 2 atoms, 2 residues, 2 models selected > distance #3/A:808@NH2 #6/B:3@OP1 Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 808 NH2 and 7waz (CasX2 state II.cif #6/B DT 3 OP1: 3.209Å > select #6/B 614 atoms, 686 bonds, 30 residues, 1 model selected > color sel hot pink > ui tool show ""Show Sequence Viewer"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > sequence chain #6/D Alignment identifier is 6/D > select #4/B:-2 20 atoms, 21 bonds, 1 residue, 1 model selected > select #4/B:-2 20 atoms, 21 bonds, 1 residue, 1 model selected Window position QRect(1985,942 575x86) outside any known screen, using primary screen The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. [Repeated 1 time(s)] > select #6/D:122 22 atoms, 24 bonds, 1 residue, 1 model selected > select #6/D:110-122 282 atoms, 317 bonds, 13 residues, 1 model selected > select #6/D:111-122 259 atoms, 291 bonds, 12 residues, 1 model selected > select #6/D:1 23 atoms, 25 bonds, 1 residue, 1 model selected > select #6/D 2446 atoms, 2734 bonds, 78 pseudobonds, 115 residues, 3 models selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. [Repeated 4 time(s)] > hide #3 models > hide #!6 models > show #1 models > show #!4 models > hide #1 models > show #1 models > hide #!4 models > hide #1 models > show #3 models > show #!6 models > select #3/A:808@NH1 1 atom, 1 residue, 1 model selected > select add #6/B:3@OP1 2 atoms, 2 residues, 2 models selected > distance #3/A:808@NH1 #6/B:3@OP1 Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 808 NH1 and 7waz (CasX2 state II.cif #6/B DT 3 OP1: 1.752Å > save ""/Users/npd1/Desktop/X2+X2MAX stateI & state II.cxs"" ——— End of log from Thu Nov 14 19:14:01 2024 ——— opened ChimeraX session > show #1 models > show #2 models > show #!4 models > show #!5 models > show #!7 models > select add #1 7923 atoms, 8081 bonds, 977 residues, 3 models selected > select add #2 15844 atoms, 16162 bonds, 1952 residues, 4 models selected > select add #3 23764 atoms, 24243 bonds, 2926 residues, 4 models selected > select add #4 35217 atoms, 36284 bonds, 6 pseudobonds, 4061 residues, 7 models selected > select add #5 46670 atoms, 48325 bonds, 9 pseudobonds, 5196 residues, 9 models selected > select add #6 57703 atoms, 59902 bonds, 145 pseudobonds, 6304 residues, 11 models selected > select add #7 67799 atoms, 70555 bonds, 307 pseudobonds, 7276 residues, 14 models selected > select add #8 67799 atoms, 70555 bonds, 339 pseudobonds, 7276 residues, 15 models selected > select subtract #8 67799 atoms, 70555 bonds, 301 pseudobonds, 7276 residues, 13 models selected > select all 67799 atoms, 70555 bonds, 339 pseudobonds, 7276 residues, 15 models selected > color #1 skyblue > select #1,2,3,4,5,6,7 67799 atoms, 70555 bonds, 339 pseudobonds, 7276 residues, 14 models selected > select #1 7921 atoms, 8081 bonds, 975 residues, 1 model selected > select #1/D 7921 atoms, 8081 bonds, 975 residues, 1 model selected > select #2/D 7921 atoms, 8081 bonds, 975 residues, 1 model selected > hide #1 models > hide #3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > hide #!8 models > select /D:4-978 25362 atoms, 26802 bonds, 146 pseudobonds, 2398 residues, 13 models selected > select all 67799 atoms, 70555 bonds, 339 pseudobonds, 7276 residues, 15 models selected > show #1 models > show #3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > select all 67799 atoms, 70555 bonds, 339 pseudobonds, 7276 residues, 15 models selected > select all 67799 atoms, 70555 bonds, 339 pseudobonds, 7276 residues, 15 models selected > color (#1-3#!4-7 & sel) cornflower blue > lighting flat > lighting full > lighting soft > lighting simple > lighting soft > set bgColor white > nucleotides sel atoms > style nucleic & sel stick Changed 14306 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 14306 atom styles > hide #2 models > hide #3 models > show #3 models > hide #3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > select #1/D:808 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel byhetero > hide #1 models > show #2 models > select #2/D:808 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel byhetero > hide #2 models > show #3 models > select #3/A:808 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel byhetero > hide #3 models > show #!4 models > select #4/A:808 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel byhetero > hide #!4 models > show #!5 models > select #5/A:808 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel cartoons > show sel atoms > color sel byhetero > hide #!5 models > show #!6 models > select #6/A:808 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel byhetero > hide #!6 models > show #!7 models > select #7/A:808 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > show #!4 models > show #!5 models > show #!6 models > select #4,5,6,7/B 2636 atoms, 2945 bonds, 129 residues, 4 models selected > color sel light gray > color sel byhetero > nucleotides sel slab > style nucleic & sel stick Changed 2636 atom styles > nucleotides sel slab > style nucleic & sel stick Changed 2636 atom styles > nucleotides sel slab > style nucleic & sel stick Changed 2636 atom styles > hide sel atoms [Repeated 1 time(s)] > show sel atoms > nucleotides sel stubs > nucleotides sel ladder > nucleotides sel tube/slab shape muffler > show sel atoms > nucleotides sel slab > style nucleic & sel stick Changed 2636 atom styles > nucleotides sel tube/slab shape box > select #4,5,6,7/C 1886 atoms, 2106 bonds, 93 residues, 4 models selected > nucleotides sel tube/slab shape box > color sel dark gray > color sel dim gray > show sel atoms [Repeated 2 time(s)] > color sel byhetero > nucleotides sel tube/slab shape box > hide sel cartoons > select #4,5,6,7/D 9784 atoms, 10936 bonds, 165 pseudobonds, 460 residues, 10 models selected > hide sel cartoons > hide sel atoms [Repeated 1 time(s)] > select #4,5,6,7/C 1886 atoms, 2106 bonds, 93 residues, 4 models selected > select #4,5,6,7/C 1886 atoms, 2106 bonds, 93 residues, 4 models selected > select #4,5,6,7/B 2636 atoms, 2945 bonds, 129 residues, 4 models selected > hide sel cartoons > select clear > select #1/D:808 11 atoms, 10 bonds, 1 residue, 1 model selected > show #3 models > show #2 models > show #1 models > hide #2 models > hide #!7 models > hide #!5 models > save ""/Users/npd1/Desktop/Session 1.cxs"" > select #1,3,4,6 38329 atoms, 39780 bonds, 166 pseudobonds, 4194 residues, 8 models selected > cartoon style (#1,3#!4,6 & sel) modeHelix tube sides 20 > cartoon style (#1,3#!4,6 & sel & coil) xsection oval > cartoon style (#1,3#!4,6 & sel) xsection barbell modeHelix default > cartoon style (#1,3#!4,6 & sel) modeHelix tube sides 20 > select #6/B:1-30 614 atoms, 686 bonds, 30 residues, 1 model selected > select #6/C:1-12 245 atoms, 273 bonds, 12 residues, 1 model selected > select #6/B:1-30 614 atoms, 686 bonds, 30 residues, 1 model selected > select #1,3,4,6/B 1288 atoms, 1439 bonds, 63 residues, 2 models selected > color sel white > color sel byhetero > select clear > graphics silhouettes false > graphics silhouettes true > lighting shadows true intensity 0.5 > lighting shadows false > select #1/D:808 11 atoms, 10 bonds, 1 residue, 1 model selected > hide #3 models > hide #!4 models > hide #!6 models > show #!6 models > show #!4 models > show #3 models > save ""/Users/npd1/Desktop/Session 2.cxs"" ——— End of log from Tue Dec 17 15:14:27 2024 ——— opened ChimeraX session > select #4,6/B,C,D 6972 atoms, 7791 bonds, 131 pseudobonds, 332 residues, 5 models selected > hide sel cartoons > hide sel atoms > select #4,6/A 15515 atoms, 15827 bonds, 5 pseudobonds, 1912 residues, 4 models selected > hide sel atoms > show sel surfaces [Repeated 1 time(s)] > hide sel cartoons [Repeated 2 time(s)] > select #1,3/D 7921 atoms, 8081 bonds, 975 residues, 1 model selected > hide sel cartoons > hide sel atoms > show sel surfaces > select #1/D:119@CA 1 atom, 1 residue, 1 model selected > hide #!1 models > hide #!4 models > hide #!6 models > select #3/D Nothing selected > select #3/A 7921 atoms, 8081 bonds, 975 residues, 1 model selected > hide sel cartoons > show sel surfaces > hide sel atoms > show #!1 models > show #!4 models > show #!6 models > select #3,4,6/A 23436 atoms, 23908 bonds, 5 pseudobonds, 2887 residues, 5 models selected > select #3,4,6/A:768,856,764,904955 99 atoms, 90 bonds, 9 residues, 3 models selected > save ""/Users/npd1/Desktop/Session 3 surfaces.cxs"" > select #3,4,6/A:768,856,764,904,955 159 atoms, 144 bonds, 15 residues, 3 models selected > select #3,4,6/A:768,856,764,904,955,898 186 atoms, 168 bonds, 18 residues, 3 models selected > color (#!3-4,6 & sel) red > select #1/D:768,856,764,904,955,898 62 atoms, 56 bonds, 6 residues, 1 model selected > color (#!1 & sel) red > select #1/D:808 11 atoms, 10 bonds, 1 residue, 1 model selected > color (#!1 & sel) hot pink > select #3,4,6/A:808 29 atoms, 26 bonds, 3 residues, 3 models selected > select #3,4,6/A:808 29 atoms, 26 bonds, 3 residues, 3 models selected > color (#!3-4,6 & sel) magenta > save ""/Users/npd1/Desktop/Session 3a surfaces.cxs"" ——— End of log from Tue Dec 17 16:34:16 2024 ——— opened ChimeraX session > select #3,4,6/A:191-340 3522 atoms, 3597 bonds, 450 residues, 3 models selected > hide sel surfaces > select #1/D:191-340 1174 atoms, 1199 bonds, 150 residues, 1 model selected > hide sel surfaces > hide #!3 models > hide #!6 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > show #!3 models > show #!6 models > select #3,4,6/A:808 29 atoms, 26 bonds, 3 residues, 3 models selected > color (#!3-4,6 & sel) magenta > select #1/D:808 11 atoms, 10 bonds, 1 residue, 1 model selected > color (#!1 & sel) magenta > hide #!1 models > show #!1 models > hide #!3 models > hide #!6 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > select clear > hide #!1 models > show #!1 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > save /Users/npd1/Desktop/image1.png supersample 3 > hide #!1 models > show #!4 models > save /Users/npd1/Desktop/image2.png supersample 3 > show #!1 models > hide #!4 models > hide #!1 models > show #!6 models > hide #!6 models > show #!6 models > save /Users/npd1/Desktop/image1.png supersample 3 > hide #!6 models > show #!3 models > save /Users/npd1/Desktop/image2.png supersample 3 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!1 models > show #!4 models > select #3,4,6/B,C 2080 atoms, 2323 bonds, 26 pseudobonds, 102 residues, 3 models selected > show sel & #!4 cartoons > show #!6 models > select #3,4,6/B,C 2080 atoms, 2323 bonds, 26 pseudobonds, 102 residues, 3 models selected > show sel cartoons > save ""/Users/npd1/Desktop/Session 3b surfaces.cxs"" > hide #!6 models > select clear > select #3,4,6/B,C 2080 atoms, 2323 bonds, 26 pseudobonds, 102 residues, 3 models selected > show #!6 models > select #3,4,6/B,C 2080 atoms, 2323 bonds, 26 pseudobonds, 102 residues, 3 models selected > nucleotides sel stubs [Repeated 1 time(s)] > show sel cartoons > show sel atoms > select clear > hide #!6 models > show #!6 models > select #3,4,6/B,C 2080 atoms, 2323 bonds, 26 pseudobonds, 102 residues, 3 models selected > nucleotides sel atoms > style nucleic & sel stick Changed 2080 atom styles > nucleotides sel ladder [Repeated 1 time(s)] > nucleotides sel tube/slab shape box > select #6/A:887@CD 1 atom, 1 residue, 1 model selected > select clear > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > save /Users/npd1/Desktop/image1.png supersample 3 > hide #!6 models > show #!4 models > save /Users/npd1/Desktop/image2.png supersample 3 > show #!1 models > select #4/A 7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected > hide sel surfaces [Repeated 1 time(s)] > save /Users/npd1/Desktop/image1.png supersample 3 > hide #!1 models > show #!3 models > hide #!4 models > show #!6 models > select #6/A 7729 atoms, 7884 bonds, 3 pseudobonds, 952 residues, 2 models selected > hide sel surfaces > save /Users/npd1/Desktop/image1.png supersample 3 Unsupported scale factor (0.000000) detected on Display0 [Repeated 1 time(s)] > hide #!6 models > show #!6 models > hide #!3 models > show #!3 models > select #3/A 7921 atoms, 8081 bonds, 975 residues, 1 model selected > select #3/D Nothing selected > select #3/A 7921 atoms, 8081 bonds, 975 residues, 1 model selected > select #3/A:1-60 470 atoms, 474 bonds, 57 residues, 1 model selected > color (#!3 & sel) cornflower blue > select #3/A:60-100,191-340 1512 atoms, 1543 bonds, 191 residues, 1 model selected > color (#!3 & sel) yellow > select #3/A:100-191 727 atoms, 743 bonds, 92 residues, 1 model selected > color (#!3 & sel) red > select #3/A:340-496 1316 atoms, 1345 bonds, 157 residues, 1 model selected > color (#!3 & sel) orange > select #3/A:643-696,750-811,918-978 1433 atoms, 1461 bonds, 177 residues, 1 model selected > color (#!3 & sel) forest green > select #3/A:696-760 530 atoms, 535 bonds, 65 residues, 1 model selected > color (#!3 & sel) blue > select #3/A:811-918 870 atoms, 883 bonds, 108 residues, 1 model selected > color (#!3 & sel) magenta > select #3,4,6/A:768,856,764,904,955,898 186 atoms, 168 bonds, 18 residues, 3 models selected > color (#!3,6 & sel) red > select #3,4,6/A:808 29 atoms, 26 bonds, 3 residues, 3 models selected > color (#!3,6 & sel) purple > select #3,4,6/A:756,659,922 55 atoms, 46 bonds, 9 residues, 3 models selected > color (#!3,6 & sel) light sea green > color (#!3,6 & sel) yellow > select #3,4,6/A:922 18 atoms, 15 bonds, 3 residues, 3 models selected > hide #!3 models > hide #!6 models > show #!4 models > show #!1 models > select #1/D:756,659,922 25 atoms, 22 bonds, 3 residues, 1 model selected > color (#!1 & sel) yellow > select clear > save /Users/npd1/Desktop/image1.png supersample 3 > show #!6 models > show #!3 models > hide #!4 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > select #3/A:808@NH2 1 atom, 1 residue, 1 model selected > ui tool show Distances > select add #3/A:756@OE1 2 atoms, 2 residues, 2 models selected > distance #3/A:808@NH2 #3/A:756@OE1 Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 808 NH2 and GLU 756 OE1: 10.332Å > hide #!6 models > hide #!3 models > show #!4 models > show #!1 models > select #1/D:756@OE1 1 atom, 1 residue, 1 model selected > select add #1/D:808@NH2 2 atoms, 2 residues, 2 models selected > distance #1/D:756@OE1 #1/D:808@NH2 Distance between X2-Max 7WAY (state I).pdb #1/D GLU 756 OE1 and ARG 808 NH2: 9.723Å > save ""/Users/npd1/Desktop/Session 4 surfaces.cxs"" > select #1/D 7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected > color (#!1 & sel) cornflower blue > select #1/D:26,610 22 atoms, 20 bonds, 2 residues, 1 model selected > color (#!1 & sel) red > select #4 11453 atoms, 12041 bonds, 6 pseudobonds, 1135 residues, 3 models selected > select #4/A 7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected > show sel surfaces > select #4/A 7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected > color (#!4 & sel) cornflower blue > hide #!1 models > select #4/A:26,610 16 atoms, 14 bonds, 2 residues, 1 model selected > color (#!4 & sel) red > ui tool show ""Show Sequence Viewer"" > sequence chain #4/B Alignment identifier is 4/B > sequence chain #4/C Alignment identifier is 4/C > select #4/C:6 20 atoms, 21 bonds, 1 residue, 1 model selected > select #4/C:6-9 79 atoms, 86 bonds, 4 residues, 1 model selected > select #4/C:8 20 atoms, 21 bonds, 1 residue, 1 model selected > select #4/C:8-10 60 atoms, 66 bonds, 3 residues, 1 model selected > select clear > select #4/B:-2-0 60 atoms, 66 bonds, 3 residues, 1 model selected > select #4/C:7 20 atoms, 21 bonds, 1 residue, 1 model selected > select #4/C:7-9 59 atoms, 64 bonds, 3 residues, 1 model selected > select #4/C:7 20 atoms, 21 bonds, 1 residue, 1 model selected > select #4/C:7-10 80 atoms, 88 bonds, 4 residues, 1 model selected > color sel hot pink > save /Users/npd1/Desktop/T26-K610.cxs > select #4/A:562-568 52 atoms, 51 bonds, 7 residues, 1 model selected > select #4/A:561-568 60 atoms, 59 bonds, 8 residues, 1 model selected > hide sel surfaces > undo > select #4/A:561-568 60 atoms, 59 bonds, 8 residues, 1 model selected > show sel surfaces > select #4/A:562-568 52 atoms, 51 bonds, 7 residues, 1 model selected > hide sel surfaces > show sel surfaces > select #4/A:563-568 43 atoms, 42 bonds, 6 residues, 1 model selected > hide sel surfaces > show sel surfaces > select #4/A:564-568 34 atoms, 33 bonds, 5 residues, 1 model selected > select #4/A:563-568 43 atoms, 42 bonds, 6 residues, 1 model selected > select #4/A:562-568 52 atoms, 51 bonds, 7 residues, 1 model selected > hide sel surfaces > select #4/A:26,610 16 atoms, 14 bonds, 2 residues, 1 model selected > color (#!4 & sel) magenta > select #4/A:26 7 atoms, 6 bonds, 1 residue, 1 model selected > color (#!4 & sel) orange > select #4/A:610@CD 1 atom, 1 residue, 1 model selected > select #4/A:603@CA 1 atom, 1 residue, 1 model selected > select clear > save /Users/npd1/Desktop/image2.png supersample 3 > save /Users/npd1/Desktop/image3.png supersample 3 > select #4/A:562-568 52 atoms, 51 bonds, 7 residues, 1 model selected > show sel surfaces > hide sel surfaces > show sel surfaces > transparency (#!4 & sel) 80 > hide sel surfaces > save /Users/npd1/Desktop/image4.png supersample 3 > show #!1 models > select #1/D:562-568 52 atoms, 51 bonds, 7 residues, 1 model selected > hide sel surfaces > select #4/A:26,610 16 atoms, 14 bonds, 2 residues, 1 model selected > color (#!4 & sel) magenta > select #1/D:610 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/D 7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected > show sel surfaces > select #1/D:610 11 atoms, 10 bonds, 1 residue, 1 model selected > color (#!1 & sel) magenta > select #1/D:26 11 atoms, 10 bonds, 1 residue, 1 model selected > color (#!1 & sel) orange > select #4/A 7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected > hide sel surfaces > select #1/D 7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected > select #1/D 7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected > select #1/D:562-568 52 atoms, 51 bonds, 7 residues, 1 model selected > hide sel surfaces > show sel surfaces > select #1/D:563-568 43 atoms, 42 bonds, 6 residues, 1 model selected > select #1/D:563-567 36 atoms, 35 bonds, 5 residues, 1 model selected > hide sel surfaces > select #1/D:563 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel surfaces > hide sel surfaces > select #1/D:564 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel surfaces > hide sel surfaces > select #1/D:565 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel surfaces > select #1/D:566 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel surfaces > select #1/D:567 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel surfaces > select #1/D:568 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel surfaces > select #1/D:569 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/D:561 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/D:562 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/D:563 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel surfaces > select #1/D:564 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel surfaces > select #1/D 7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected > show sel surfaces > select #1/D:191:340 17 atoms, 15 bonds, 2 residues, 1 model selected > select #1/D:191:340 17 atoms, 15 bonds, 2 residues, 1 model selected > hide sel surfaces > show sel surfaces > select #1/D:191:340 17 atoms, 15 bonds, 2 residues, 1 model selected > select #1/D 7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected > select #1/D:191-340 1174 atoms, 1199 bonds, 150 residues, 1 model selected > hide sel surfaces > lighting soft > lighting full > lighting simple > select #1/D 7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected > show sel surfaces > hide sel surfaces > show sel cartoons > select #1/D:26,610 22 atoms, 20 bonds, 2 residues, 1 model selected > show sel cartoons > show sel atoms > select #4/B,C 1221 atoms, 1364 bonds, 60 residues, 1 model selected > hide sel cartoons > color sel byhetero > select #1/D:26 11 atoms, 10 bonds, 1 residue, 1 model selected > color (#!1 & sel) forest green > color sel byhetero > select #1/D:610 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel byhetero > select #1/D 7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected > show sel surfaces > select #1/D:26,610 22 atoms, 20 bonds, 2 residues, 1 model selected > transparency (#!1 & sel) 70 > select #1/D:563 9 atoms, 8 bonds, 1 residue, 1 model selected > transparency (#!1 & sel) 70 > show sel atoms > select #4/C,D 2993 atoms, 3345 bonds, 1 pseudobond, 142 residues, 2 models selected > show sel cartoons > select #4/B,C 1221 atoms, 1364 bonds, 60 residues, 1 model selected > show sel cartoons > select #1/D:25@CA 1 atom, 1 residue, 1 model selected > select #1/D:26@NH2 1 atom, 1 residue, 1 model selected > select #1/D:191@NE2 1 atom, 1 residue, 1 model selected > select #1/D:642@O 1 atom, 1 residue, 1 model selected > select #1/D:25 9 atoms, 8 bonds, 1 residue, 1 model selected > transparency (#!1 & sel) 70 > show sel cartoons > show sel atoms > select #1/D:642@NH1 1 atom, 1 residue, 1 model selected > select clear > select #1/D:610 11 atoms, 10 bonds, 1 residue, 1 model selected > transparency (#!1 & sel) 0 > color (#!1 & sel) cornflower blue > select clear > save /Users/npd1/Desktop/image5.png supersample 3 > hide #!1 models > select #4/A 7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected > show sel surfaces > color (#!4 & sel) cornflower blue > select #4/A:26 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/A:26,25,563 25 atoms, 23 bonds, 3 residues, 1 model selected > transparency (#!4 & sel) 70 > show sel atoms > select #4/A:26 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel byhetero [Repeated 4 time(s)] > color (#!4 & sel) forest green > color sel byhetero > select #4/A:613@ND2 1 atom, 1 residue, 1 model selected Drag select of 7way (CasX2 state I).pdb_A SES surface, 186 of 1019076 triangles > select #4/A:195-400 1652 atoms, 1690 bonds, 206 residues, 1 model selected > hide sel surfaces > select #4/A:164-400 1840 atoms, 1882 bonds, 1 pseudobond, 229 residues, 2 models selected > hide sel surfaces > select #4/A:132-400 2102 atoms, 2151 bonds, 1 pseudobond, 261 residues, 2 models selected > select #4/A:99-400 2298 atoms, 2350 bonds, 2 pseudobonds, 287 residues, 2 models selected > hide sel surfaces > hide #!4 models > show #!4 models > select #4/A 7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected > show sel atoms > select #4/A:99-400 2298 atoms, 2350 bonds, 2 pseudobonds, 287 residues, 2 models selected > hide sel atoms > select #4/A:98-400 2304 atoms, 2356 bonds, 2 pseudobonds, 288 residues, 2 models selected > hide sel surfaces > hide sel atoms > select #4/A:8-400 3042 atoms, 3106 bonds, 2 pseudobonds, 378 residues, 2 models selected > hide sel atoms > undo > select #4/A:88-400 2384 atoms, 2438 bonds, 2 pseudobonds, 298 residues, 2 models selected > hide sel surfaces > hide sel atoms > save /Users/npd1/Desktop/image6.png supersample 3 > select #4/A:563 9 atoms, 8 bonds, 1 residue, 1 model selected > transparency (#!4 & sel) 0 > select #4/A:25 9 atoms, 8 bonds, 1 residue, 1 model selected > transparency (#!4 & sel) 0 > select clear > select #4/A:26 7 atoms, 6 bonds, 1 residue, 1 model selected > transparency (#!4 & sel) 80 > lighting soft > lighting simple > lighting full > lighting flat > lighting simple > lighting shadows true > lighting simple > save /Users/npd1/Desktop/image7.png supersample 3 > select clear > save /Users/npd1/Desktop/image8.png supersample 3 > save /Users/npd1/Desktop/T26.cxs ——— End of log from Wed Dec 18 17:53:52 2024 ——— opened ChimeraX session > select #4/D 2446 atoms, 2734 bonds, 1 pseudobond, 115 residues, 2 models selected > show sel cartoons > nucleotides sel atoms > style nucleic & sel stick Changed 2446 atom styles > nucleotides sel ladder [Repeated 3 time(s)] > show sel atoms > nucleotides sel ladder [Repeated 1 time(s)] > nucleotides sel tube/slab shape box > select #4/A:28@CB 1 atom, 1 residue, 1 model selected > select clear > select #4/A 7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected > select #4/A:85 12 atoms, 12 bonds, 1 residue, 1 model selected > hide sel surfaces > select #4/D 2446 atoms, 2734 bonds, 1 pseudobond, 115 residues, 2 models selected > color (#!4 & sel) orange > select #4/A:29@CG 1 atom, 1 residue, 1 model selected > select clear > save /Users/npd1/Desktop/image11.png supersample 3 > save /Users/npd1/Desktop/T26a.cxs ——— End of log from Wed Dec 18 18:16:40 2024 ——— opened ChimeraX session > select #4/A 7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected > select #4/A:26 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel surfaces [Repeated 1 time(s)] > transparency (#!4 & sel) 0 > color (#!4 & sel) cornflower blue > select #4/A:610 9 atoms, 8 bonds, 1 residue, 1 model selected > transparency (#!4 & sel) 80 > color (#!4 & sel) forest green > color sel byhetero > select #4/A 7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected > show sel surfaces > select #4/A:613@CB 1 atom, 1 residue, 1 model selected > select #4/A:643@CB 1 atom, 1 residue, 1 model selected > select #4/A:22@CD 1 atom, 1 residue, 1 model selected > select #4/A:24@CA 1 atom, 1 residue, 1 model selected > select #1 7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected > save /Users/npd1/Desktop/image1.png supersample 3 > save /Users/npd1/Desktop/K610.cxs ——— End of log from Thu Dec 19 08:04:12 2024 ——— opened ChimeraX session > select #4/A 7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected > hide sel atoms > hide sel cartoons > hide sel surfaces > select #1/D 7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected > show #!4 atoms > show #!4 surfaces > select #4/B,C,D 3667 atoms, 4098 bonds, 1 pseudobond, 175 residues, 2 models selected > hide sel surfaces > select #4/A 7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected > hide sel surfaces > hide sel cartoons > hide sel atoms > select #1/D 7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected > show #!1 models > select #4/A 7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected > hide sel surfaces > hide sel cartoons > hide sel atoms > select #4/A 7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected > transparency (#!4 & sel) 0 > select #4/D 2446 atoms, 2734 bonds, 1 pseudobond, 115 residues, 2 models selected > select #1/D 7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected > transparency (#!1 & sel) 0 > select #1/D:26 11 atoms, 10 bonds, 1 residue, 1 model selected > transparency (#!1 & sel) 80 > save /Users/npd1/Desktop/R610.cxs > select #1/D:25 9 atoms, 8 bonds, 1 residue, 1 model selected > surface hidePatches (#!1 & sel) > select #1/D:563 9 atoms, 8 bonds, 1 residue, 1 model selected > transparency (#!1 & sel) 80 > select #1/D:25 9 atoms, 8 bonds, 1 residue, 1 model selected > transparency (#!1 & sel) 80 > show sel surfaces > select clear > save /Users/npd1/Desktop/R610.cxs > save /Users/npd1/Desktop/image2.png supersample 3 > select #1/D:25,563 18 atoms, 16 bonds, 2 residues, 1 model selected > color sel byhetero > hide sel surfaces > show sel surfaces > select clear [Repeated 1 time(s)] > save /Users/npd1/Desktop/R610.cxs ——— End of log from Thu Dec 19 08:17:31 2024 ——— opened ChimeraX session > select #1/D 7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected > color (#!1 & sel) cornflower blue > transparency (#!1 & sel) 0 > select #1/D:610 11 atoms, 10 bonds, 1 residue, 1 model selected > transparency (#!1 & sel) 80 > color (#!1 & sel) forest green > color sel byhetero > ui tool show Rotamers Populating font family aliases took 70 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > swapaa interactive sel ARG rotLib Dunbrack X2-Max 7WAY (state I).pdb #1/D ARG 610: phi -126.4, psi 147.2 trans Changed 600 bond radii > select up 123 atoms, 123 bonds, 15 residues, 2 models selected > save /Users/npd1/Desktop/R610.cxs ——— End of log from Thu Dec 19 08:48:26 2024 ——— opened ChimeraX session > select #1/D:563-564 15 atoms, 14 bonds, 2 residues, 1 model selected > transparency (#!1 & sel) 80 > ui tool show Rotamers > select #1/D:610 11 atoms, 10 bonds, 1 residue, 1 model selected > select #4/B 674 atoms, 753 bonds, 33 residues, 1 model selected > hide sel cartoons > select #1/D:610 11 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel ARG rotLib Dunbrack X2-Max 7WAY (state I).pdb #1/D ARG 610: phi -126.4, psi 147.2 trans Changed 600 bond radii > select #1.2.23/A:1@NH2 1 atom, 1 residue, 1 model selected > select add #!1/D:563@CE 2 atoms, 2 residues, 2 models selected > select add #4/B:22@OP1 3 atoms, 3 residues, 4 models selected > select #1.2.48/A:1@NH2 1 atom, 1 residue, 1 model selected > select add #1.2.23/A:1@NH2 2 atoms, 2 residues, 2 models selected > select #1.2.23/A:1@NH2 1 atom, 1 residue, 1 model selected > select add #4/B:22@OP1 2 atoms, 2 residues, 2 models selected > ui tool show Distances > distance #1.2.23/A:1@NH2 #4/B:22@OP1 Distance between rotamer 23 #1.2.23/A ARG 1 NH2 and 7way (CasX2 state I).pdb #4/B DG 22 OP1: 2.632Å > distance #1.2.23/A:1@NH2 #4/B:22@OP1 Distance already exists; modify distance properties with 'distance style' > select #1.2.57/A:1@NH2 1 atom, 1 residue, 1 model selected > select add #4/B:22@OP1 2 atoms, 2 residues, 2 models selected > distance #1.2.57/A:1@NH2 #4/B:22@OP1 Distance between rotamer 57 #1.2.57/A ARG 1 NH2 and 7way (CasX2 state I).pdb #4/B DG 22 OP1: 2.451Å > select #1.2.48/A:1@NH2 1 atom, 1 residue, 1 model selected > select add #4/B:22@OP1 2 atoms, 2 residues, 2 models selected > distance #1.2.48/A:1@NH2 #4/B:22@OP1 Distance between rotamer 48 #1.2.48/A ARG 1 NH2 and 7way (CasX2 state I).pdb #4/B DG 22 OP1: 2.329Å > swapaa #!1/D:610 ARG criteria 48 rotLib Dunbrack retain false Using Dunbrack library X2-Max 7WAY (state I).pdb #!1/D ARG 610: phi -126.4, psi 147.2 trans Applying ARG rotamer (chi angles: -170.4 -85.5 -170.4 -173.1) to X2-Max 7WAY (state I).pdb #!1/D ARG 610 > select #1/D:612 5 atoms, 4 bonds, 1 residue, 1 model selected > hide sel surfaces > select #1/D 7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected > hide sel surfaces > select #1/D:611 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #1/D:612 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #1/D:610 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/D:611 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/D:610 11 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel ARG rotLib Dunbrack X2-Max 7WAY (state I).pdb #1/D ARG 610: phi -126.4, psi 147.2 trans Changed 600 bond radii Drag select of 1 atoms, 1 residues > select #1.2.57/A:1@NH2 1 atom, 1 residue, 1 model selected > select add #4/B:22@OP1 2 atoms, 2 residues, 2 models selected > distance #1.2.57/A:1@NH2 #4/B:22@OP1 Distance between rotamer 57 #1.2.57/A ARG 1 NH2 and 7way (CasX2 state I).pdb #4/B DG 22 OP1: 2.453Å > select #1.2.23/A:1@NH2 1 atom, 1 residue, 1 model selected > select add #4/B:22@OP1 2 atoms, 2 residues, 2 models selected > distance #1.2.23/A:1@NH2 #4/B:22@OP1 Distance between rotamer 23 #1.2.23/A ARG 1 NH2 and 7way (CasX2 state I).pdb #4/B DG 22 OP1: 2.633Å > swapaa #!1/D:610 ARG criteria 23 rotLib Dunbrack retain false Using Dunbrack library X2-Max 7WAY (state I).pdb #!1/D ARG 610: phi -126.4, psi 147.2 trans Applying ARG rotamer (chi angles: -178.6 176.8 -178.6 -89.1) to X2-Max 7WAY (state I).pdb #!1/D ARG 610 > select #1/D 7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected > show sel surfaces > select #1/D:610 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel surfaces > select #1/D:610@NH2 1 atom, 1 residue, 1 model selected > select add #4/B:22@OP1 2 atoms, 2 residues, 3 models selected > distance #1/D:610@NH2 #4/B:22@OP1 Distance between X2-Max 7WAY (state I).pdb #1/D ARG 610 NH2 and 7way (CasX2 state I).pdb #4/B DG 22 OP1: 2.633Å > show #!8 models > ~distance #1/D:610@NH2 #4/B:22@OP1 > ~distance #1/D:26@NH2 #4/B:21@OP1 > ~distance #3/A:26@NH2 #4/C:11@O2 > ~distance #3/A:26@NH2 #4/B:20@OP1 > ~distance #1/D:26@NH2 #3/A:26@NH2 > ~distance #4/A:610@NZ #4/B:22@OP1 > ~distance #4/B:20@OP1 #1/D:26@NH2 > ~distance #3/A:610@NH1 #4/B:22@OP1 > ~distance #3/A:808@NH1 #6/B:3@OP1 > ~distance #1/D:26@NH2 #4/B:20@OP2 > ~distance #4/C:21@OP2 #1/D:808@NH1 > ~distance #6/A:610@NZ #6/B:22@OP1 > ~distance #1/D:808@NH2 #4/C:21@OP2 > ~distance #6/B:21@OP1 #2/D:26@NH2 > ~distance #4/A:610@NZ #4/B:21@OP2 > ~distance #2/D:26@NH2 #6/B:21@OP2 > ~distance #2/D:610@NH1 #6/B:21@OP2 > ~distance #6/A:808@NZ #6/B:3@OP1 > ~distance #2/D:610@NH1 #6/B:22@OP1 > ~distance #3/A:26@NH2 #4/B:21@OP2 > ~distance #6/B:20@OP1 #2/D:26@NH2 > ~distance #3/A:26@NH2 #6/C:11@O2 > ~distance #6/A:610@NZ #6/B:21@OP2 > ~distance #3/A:26@NH2 #6/B:20@OP1 > ~distance #3/A:26@NH2 #6/B:21@OP1 > ~distance #1/D:26@NH2 #2/D:26@NH2 > ~distance #6/A:610@NZ #2/D:610@NH1 > ~distance #1/D:26@NH2 #4/C:12@O2 > ~distance #3/A:26@NH1 #6/B:21@OP1 > ~distance #4/A:808@NZ #4/C:21@OP2 > ~distance #2/D:26@NH2 #6/C:12@O2 > ~distance #3/A:26@NH2 #6/C:12@O2 > ~distance #3/A:808@NH2 #6/B:3@OP1 > ~distance #1/D:756@OE1 #1/D:808@NH2 > ~distance #3/A:808@NH2 #3/A:756@OE1 > ~distance #3/A:26@NH2 #4/B:20@OP2 > ~distance #3/A:26@NH2 #4/B:21@OP1 > ~distance #1/D:26@NH2 #4/C:11@O2 > ~distance #1/D:26@NH2 #4/B:21@OP2 > ui tool show Distances > distance #1/D:610@NH2 #4/B:22@OP1 Distance between X2-Max 7WAY (state I).pdb #1/D ARG 610 NH2 and 7way (CasX2 state I).pdb #4/B DG 22 OP1: 2.633Å > select #1/D:608@CA 1 atom, 1 residue, 1 model selected > select #2 7921 atoms, 8081 bonds, 975 residues, 1 model selected > save /Users/npd1/Desktop/R610.cxs > save /Users/npd1/Desktop/image7.png supersample 3 > hide #!1 models > select #4/A 7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected > show sel surfaces > select #4/A:610 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel surfaces > show sel atoms > select #4/A:610@NZ 1 atom, 1 residue, 1 model selected > select add #4/B:22@OP1 2 atoms, 2 residues, 2 models selected > distance #4/A:610@NZ #4/B:22@OP1 Distance between 7way (CasX2 state I).pdb #4/A LYS 610 NZ and /B DG 22 OP1: 4.707Å > show sel surfaces > hide sel surfaces > select #4/A:610 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel surfaces > transparency (#!4 & sel) 80 > save /Users/npd1/Desktop/K610.cxs > select clear > save /Users/npd1/Desktop/image8.png supersample 3 > save /Users/npd1/Desktop/K610a.cxs > show #!1 models > select #4/A 7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected > show sel surfaces > hide sel surfaces > hide sel cartoons > hide sel atoms > select #1/D:610 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel surfaces > transparency (#!1 & sel) 80 > select clear > save /Users/npd1/Desktop/R610a.cxs ——— End of log from Thu Dec 19 09:27:48 2024 ——— opened ChimeraX session > select #4/A:563-4 Nothing selected > select #1/D:563-4 Nothing selected > select #1/D:563-564 15 atoms, 14 bonds, 2 residues, 1 model selected > transparency (#!1 & sel) 80 > select #1/D:227@NZ 1 atom, 1 residue, 1 model selected > select clear > select #1/D:563-566 28 atoms, 27 bonds, 4 residues, 1 model selected > hide sel cartoons > hide sel atoms > hide sel surfaces > select #1/D:562-566 37 atoms, 36 bonds, 5 residues, 1 model selected > hide sel surfaces > hide sel cartoons > hide sel atoms > select #1/D:22-26 38 atoms, 37 bonds, 5 residues, 1 model selected > hide sel surfaces > hide sel cartoons > hide sel atoms > select #1/D:561-566 45 atoms, 44 bonds, 6 residues, 1 model selected > hide sel surfaces > hide sel cartoons > hide sel atoms > select #1/D:561-566,642 56 atoms, 54 bonds, 7 residues, 1 model selected > hide sel surfaces > hide sel cartoons > hide sel atoms > select #1/D:561-566,640-642 76 atoms, 74 bonds, 9 residues, 1 model selected > hide sel cartoons > hide sel atoms > hide sel surfaces > select #1/D:561-566,640-642,509 87 atoms, 85 bonds, 10 residues, 1 model selected > hide sel surfaces > hide sel cartoons > hide sel atoms > select #1/D:561-566,640-642,509,610 98 atoms, 95 bonds, 11 residues, 1 model selected > hide sel surfaces > select #1/D:561-566,640-642,509 87 atoms, 85 bonds, 10 residues, 1 model selected > show sel surfaces > show sel cartoons > show sel atoms [Repeated 1 time(s)] > show sel cartoons > transparency (#!1 & sel) 0 > select #1/D:64@CG 1 atom, 1 residue, 1 model selected > select #1/D:640-642 31 atoms, 30 bonds, 3 residues, 1 model selected > hide sel surfaces > hide sel cartoons > hide sel atoms > select #1/D:640-642,563 40 atoms, 38 bonds, 4 residues, 1 model selected > hide sel surfaces > hide sel cartoons > hide sel atoms > select #1/D:509 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel surfaces [Repeated 1 time(s)] > select #1/D 7921 atoms, 8081 bonds, 975 residues, 1 model selected > show sel surfaces [Repeated 1 time(s)] > select #1/D 7921 atoms, 8081 bonds, 975 residues, 1 model selected > transparency (#!1 & sel) 0 > hide sel surfaces > hide sel atoms > select #1/D:610 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel cartoons > show sel atoms > select #1/D 7921 atoms, 8081 bonds, 975 residues, 1 model selected > cartoon style (#!1 & sel) modeHelix tube sides 20 > label height 3 > label height 2 > label height 1 > select clear > label size 1000 > label size 1 > label size 20 > label size 30 > label size 40 > label size 2.5 Invalid ""size"" argument: Expected 'default' or an integer > label size 3 > label size 2 > label size 40 > label height 3 > label height 2.5 > label height 2 > label height 1.5 > label height 1 > label height 1.25 > select clear > save /Users/npd1/Desktop/image5.png supersample 3 > save /Users/npd1/Desktop/R610b.cxs ——— End of log from Thu Dec 19 14:32:51 2024 ——— opened ChimeraX session > select #4/A 7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected > select #1/D 7921 atoms, 8081 bonds, 975 residues, 1 model selected > cartoon style (#!1 & sel) xsection oval modeHelix default > label size 1 > label label height 1 Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > label height 1 > label height 0 > select clear > save /Users/npd1/Desktop/image1.png supersample 3 > save /Users/npd1/Desktop/image2.png supersample 3 > hide #!1 models > select #4/A 7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected > show sel cartoons > cartoon style (#!4 & sel) xsection oval modeHelix default > select #4/A:610 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select clear > save /Users/npd1/Desktop/image3.png supersample 3 > save /Users/npd1/Desktop/K610c.cxs ——— End of log from Fri Dec 20 14:41:34 2024 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac15,12 Model Number: MC8N4LL/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 11881.120.111.0.1 OS Loader Version: 11881.120.111.0.1 Software: System Software Overview: System Version: macOS 15.5 (24F5053f) Kernel Version: Darwin 24.5.0 Time since boot: 8 hours, 23 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Display: Resolution: 2560 x 1600 UI Looks like: 2560 x 1600 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported VX3276-FHD: Resolution: 1080 x 1920 UI Looks like: 1080 x 1920 @ 60.00Hz Mirror: Off Online: Yes Rotation: 90 Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX