id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18683 Crash on Mac waking from sleep anushka.ghosh@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.6.1-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. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/anushkaghosh/Downloads/HTHP_bessy200319_C2221.pdb Chain information for HTHP_bessy200319_C2221.pdb #1 --- Chain | Description A B E | No description available C D F | No description available 64 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > set bgColor white > show cartoons Computing secondary structure > style stick Changed 7585 atom styles > hide atoms > ui tool show ""Crystal Contacts"" > crystalcontacts #1 distance 1 1 pairs of asymmetric units of HTHP_bessy200319_C2221.pdb contact at distance 1.0 A Atoms MTRIX SMTRY Unit cell MTRIXref Copies 2 0 2 0 0 -1 0 1 > crystalcontacts delete #1 > crystalcontacts #1 distance 1 rainbow false 1 pairs of asymmetric units of HTHP_bessy200319_C2221.pdb contact at distance 1.0 A Atoms MTRIX SMTRY Unit cell MTRIXref Copies 2 0 2 0 0 -1 0 1 > open > /Users/anushkaghosh/Documents/Documents/Xtal/DTHP_K40TQ47K_refine_026-coot-0.pdb Chain information for DTHP_K40TQ47K_refine_026-coot-0.pdb #3 --- Chain | Description A | No description available B E | No description available C | No description available D F | No description available 64 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!2 models > hide #!1 models > select add #3 7599 atoms, 7554 bonds, 33 pseudobonds, 577 residues, 3 models selected > show sel cartoons Computing secondary structure > style sel stick Changed 7599 atom styles > hide sel atoms > show #!1 models > select add #1 15184 atoms, 14994 bonds, 57 pseudobonds, 1253 residues, 5 models selected > ui tool show Matchmaker > matchmaker #!3 to #1 Computing secondary structure 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 HTHP_bessy200319_C2221.pdb, chain B (#1) with DTHP_K40TQ47K_refine_026-coot-0.pdb, chain B (#3), sequence alignment score = 367.7 RMSD between 73 pruned atom pairs is 0.251 angstroms; (across all 73 pairs: 0.251) > hide #!1 models > select subtract #1 7599 atoms, 7554 bonds, 33 pseudobonds, 577 residues, 3 models selected > crystalcontacts #3 distance 1 rainbow false 1 pairs of asymmetric units of DTHP_K40TQ47K_refine_026-coot-0.pdb contact at distance 1.0 A Atoms MTRIX SMTRY Unit cell MTRIXref Copies 1 0 1 0 0 0 0 1 > show #!2 models > show #!1 models > hide #!4 models > hide #!2 models > open > /Users/anushkaghosh/Documents/Documents/Xtal/HTHP_T38KK45Q_refine_014-coot-0.pdb Chain information for HTHP_T38KK45Q_refine_014-coot-0.pdb #5 --- Chain | Description A E | No description available B | No description available C D F | No description available 64 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!3 models > hide #!1 models > select subtract #3 Nothing selected > select add #5 7442 atoms, 7469 bonds, 30 pseudobonds, 506 residues, 2 models selected > show sel cartoons Computing secondary structure > style sel stick Changed 7442 atom styles > hide sel atoms > show #!1 models > show #!3 models > crystalcontacts #5 distance 1 rainbow false 0 pairs of asymmetric units of HTHP_T38KK45Q_refine_014-coot-0.pdb contact at distance 1.0 A > crystalcontacts #5 distance 2 rainbow false 6 pairs of asymmetric units of HTHP_T38KK45Q_refine_014-coot-0.pdb contact at distance 2.0 A Atoms MTRIX SMTRY Unit cell MTRIXref Copies 5 0 2 0 0 -1 0 1 2 0 7 0 0 0 0 1 2 0 7 -1 0 0 0 1 2 0 6 0 0 -1 0 1 2 0 6 0 -1 -1 0 1 1 0 2 1 0 -1 0 1 > show #!2 models > hide #!3 models > hide #!6 models > hide #!1 models > hide #!2 models > hide #!5 models > matchmaker #!5 to #1 Computing secondary structure 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 HTHP_bessy200319_C2221.pdb, chain C (#1) with HTHP_T38KK45Q_refine_014-coot-0.pdb, chain B (#5), sequence alignment score = 374 RMSD between 74 pruned atom pairs is 0.494 angstroms; (across all 74 pairs: 0.494) > show #!3 models > show #!5 models > select subtract #5 Nothing selected > show #!1 models > show #!4 models > hide #!4 models > show #!2 models > hide #!3 models > show #!3 models > hide #!2 models > show #!4 models > hide #!4 models > show #!6 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > crystalcontacts delete #5 > crystalcontacts #5 distance 1 rainbow false 0 pairs of asymmetric units of HTHP_T38KK45Q_refine_014-coot-0.pdb contact at distance 1.0 A > crystalcontacts #5 distance 2 rainbow false 6 pairs of asymmetric units of HTHP_T38KK45Q_refine_014-coot-0.pdb contact at distance 2.0 A Atoms MTRIX SMTRY Unit cell MTRIXref Copies 5 0 2 0 0 -1 0 1 2 0 7 0 0 0 0 1 2 0 7 -1 0 0 0 1 2 0 6 0 0 -1 0 1 2 0 6 0 -1 -1 0 1 1 0 2 1 0 -1 0 1 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!6 models > hide #!5 models > hide #!3 models > show #!2 models > select #1/D:40 22 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select #2.1/B:40 22 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #1/D:43 10 atoms, 9 bonds, 1 residue, 1 model selected > select #1/D:46 15 atoms, 14 bonds, 1 residue, 1 model selected > select clear > select #1/D:47 17 atoms, 16 bonds, 1 residue, 1 model selected > show sel atoms > select #2.1/B:47 17 atoms, 16 bonds, 1 residue, 1 model selected > select #1/A 1220 atoms, 1233 bonds, 4 pseudobonds, 75 residues, 2 models selected > select #1/A#2.1/A#3/A#4.1/A#5/A#6.1/A#6.2/A#6.3/A#6.4/A#6.5/A#6.6/A 13417 atoms, 13565 bonds, 55 pseudobonds, 818 residues, 24 models selected > select #1/A:47 17 atoms, 16 bonds, 1 residue, 1 model selected > show sel atoms > select #1/A:40 22 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select #1-6/A:40 226 atoms, 215 bonds, 11 residues, 11 models selected > show sel & #!1#!2.1 atoms > select #1-6/A:47 197 atoms, 186 bonds, 11 residues, 11 models selected > show sel & #!1#!2.1 atoms > select clear > color #1-2 red > undo > select #1-6/A:47 197 atoms, 186 bonds, 11 residues, 11 models selected > color (#!1#!2.1 & sel) red > select #1-6/A:40 226 atoms, 215 bonds, 11 residues, 11 models selected > color (#!1#!2.1 & sel) blue > select #1-6/A-F:40 1356 atoms, 1290 bonds, 66 residues, 11 models selected > show sel & #!1#!2.1 atoms > color (#!1#!2.1 & sel) blue > select #1-6/A-F:47 1182 atoms, 1116 bonds, 66 residues, 11 models selected > color (#!1#!2.1 & sel) red > show sel & #!1#!2.1 atoms > select #1-6/A-F:47 1182 atoms, 1116 bonds, 66 residues, 11 models selected > show hbonds > select #1-6/A-F:40 1356 atoms, 1290 bonds, 66 residues, 11 models selected > show hbonds > select clear > select #2.1/E:47@NE2 1 atom, 1 residue, 1 model selected > select #1/F:54 10 atoms, 9 bonds, 1 residue, 1 model selected > select clear > select #2.1/E:47 17 atoms, 16 bonds, 1 residue, 1 model selected > show sel target ab > select clear > show #!3 models > hide #!2 models > hide #!1 models > select #1-6/A-F:40 1356 atoms, 1290 bonds, 66 residues, 11 models selected > show sel & #!3 atoms > color (#!3 & sel) gray > color (#!3 & sel) black > select #1-6/A-F:47 1182 atoms, 1116 bonds, 66 residues, 11 models selected > color (#!3 & sel) black > show sel & #!3 atoms > show #!1 models > select clear > show #!2 models > show #!4 models > hide #!2 models > hide #!1 models > select #1-6/A-F:47 1182 atoms, 1116 bonds, 66 residues, 11 models selected > show (#!3#!4.1 & sel) target ab > select #1-6/A-F:40 1356 atoms, 1290 bonds, 66 residues, 11 models selected > show sel & #!3#!4.1 atoms > select clear > ui tool show ""Side View"" > view > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > lighting simple > lighting soft > lighting full > lighting soft > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting simple > lighting soft > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > set bgColor white > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > select ::name=""HEM"" 4818 atoms, 5016 bonds, 264 pseudobonds, 66 residues, 22 models selected > show sel & #!3#!4.1 atoms > select clear > select ::name=""HEM"" 4818 atoms, 5016 bonds, 264 pseudobonds, 66 residues, 22 models selected > color (#!3#!4.1 & sel) dark gray > select Fe 66 atoms, 66 residues, 11 models selected > style (#!3#!4.1 & sel) sphere Changed 12 atom styles > color (#!3#!4.1 & sel) black > select clear > select #1-6/A-F 81362 atoms, 82239 bonds, 324 pseudobonds, 4980 residues, 24 models selected > color (#!3#!4.1 & sel) #b4aaffff > undo > select #1-6/A-F:40 1356 atoms, 1290 bonds, 66 residues, 11 models selected > select #1-6/A-F 81362 atoms, 82239 bonds, 324 pseudobonds, 4980 residues, 24 models selected > color (#!3#!4.1 & sel) #ffaf3dff > color (#!3#!4.1 & sel) #b4aaffff > color (#!3#!4.1 & sel) #b4aafffc > color (#!3#!4.1 & sel) #b4aaffda > color (#!3#!4.1 & sel) #b4aaffd0 > color (#!3#!4.1 & sel) #b4aaffd1 > color (#!3#!4.1 & sel) #b4aaffe4 > color (#!3#!4.1 & sel) #b4aaffe7 > color (#!3#!4.1 & sel) #b4aafff0 > color (#!3#!4.1 & sel) #b4aafff1 > color (#!3#!4.1 & sel) #b4aaffff > color (#!3#!4.1 & sel) #b4aaff19 > color (#!3#!4.1 & sel) #b4aaff1b > color (#!3#!4.1 & sel) #b4aaffde > color (#!3#!4.1 & sel) #b4aaffff > color (#!3#!4.1 & sel) #b1aeffff > color (#!3#!4.1 & sel) #b3b0ffff > color (#!3#!4.1 & sel) #b5b4ffff > color (#!3#!4.1 & sel) #b5b5ffff > color (#!3#!4.1 & sel) #b7b6ffff > color (#!3#!4.1 & sel) #bab9ffff > color (#!3#!4.1 & sel) #c0bdffff > color (#!3#!4.1 & sel) #c0beffff > color (#!3#!4.1 & sel) #c2bfffff > color (#!3#!4.1 & sel) #b4aaffff > select ::name=""HEM"" 4818 atoms, 5016 bonds, 264 pseudobonds, 66 residues, 22 models selected > color (#!3#!4.1 & sel) dark gray > select Fe 66 atoms, 66 residues, 11 models selected > color (#!3#!4.1 & sel) black > select clear > select ::name=""HEM"" 4818 atoms, 5016 bonds, 264 pseudobonds, 66 residues, 22 models selected > color (#!3#!4.1 & sel) #4fb43fff > color (#!3#!4.1 & sel) #ffaf3dff > color (#!3#!4.1 & sel) #fb72f9ff > color (#!3#!4.1 & sel) #fb80f8ff > color (#!3#!4.1 & sel) #fb88f6ff > color (#!3#!4.1 & sel) #fb8df4ff > color (#!3#!4.1 & sel) #fbbdfbff > color (#!3#!4.1 & sel) #f6cefbff > color (#!3#!4.1 & sel) #f4d6fbff > color (#!3#!4.1 & sel) #fbe6f5ff > color (#!3#!4.1 & sel) #fbe7efff > color (#!3#!4.1 & sel) #fbe6eaff > color (#!3#!4.1 & sel) #fbe6e8ff > color (#!3#!4.1 & sel) #fbe6e6ff > color (#!3#!4.1 & sel) #fbe9e4ff > color (#!3#!4.1 & sel) #fbe0e5ff > color (#!3#!4.1 & sel) #e1e1e1ff > color (#!3#!4.1 & sel) #b8b8b8ff > color (#!3#!4.1 & sel) #a2a2a2ff > color (#!3#!4.1 & sel) #8c8c8cff > color (#!3#!4.1 & sel) #8f8f8fff > color (#!3#!4.1 & sel) #a9a9a9ff > color (#!3#!4.1 & sel) #afafafff > color (#!3#!4.1 & sel) #b5b5b5ff > color (#!3#!4.1 & sel) #bababaff > color (#!3#!4.1 & sel) #929292ff > color (#!3#!4.1 & sel) #707070ff > color (#!3#!4.1 & sel) #595959ff > color (#!3#!4.1 & sel) #414141ff > color (#!3#!4.1 & sel) #2b2b2bff > color (#!3#!4.1 & sel) #222222ff > color (#!3#!4.1 & sel) #212121ff > color (#!3#!4.1 & sel) #2f2f2fff > color (#!3#!4.1 & sel) #404040ff > color (#!3#!4.1 & sel) #454545ff > color (#!3#!4.1 & sel) #494949ff > color (#!3#!4.1 & sel) #505050ff > color (#!3#!4.1 & sel) #515151ff > color (#!3#!4.1 & sel) #585858ff > color (#!3#!4.1 & sel) #5b5b5bff > color (#!3#!4.1 & sel) #606060ff > color (#!3#!4.1 & sel) #626262ff > color (#!3#!4.1 & sel) #8d8d8dff > color (#!3#!4.1 & sel) #afafafff > color (#!3#!4.1 & sel) #bababaff > color (#!3#!4.1 & sel) #bcbcbcff > color (#!3#!4.1 & sel) #bdbdbdff > color (#!3#!4.1 & sel) #c9c9c9ff > color (#!3#!4.1 & sel) #cbcbcbff > color (#!3#!4.1 & sel) #cececeff > color (#!3#!4.1 & sel) #cdcdcdff > color (#!3#!4.1 & sel) #cbcbcbff > color (#!3#!4.1 & sel) #c8c8c8ff > color (#!3#!4.1 & sel) #c7c7c7ff > color (#!3#!4.1 & sel) #929292ff > color (#!3#!4.1 & sel) #a9a9a9ff > color (#!3#!4.1 & sel) #c0c0c0ff > color (#!3#!4.1 & sel) #d6d6d6ff > color (#!3#!4.1 & sel) #ebebebff > color (#!3#!4.1 & sel) #d6d6d6ff > color (#!3#!4.1 & sel) #c0c0c0ff > color (#!3#!4.1 & sel) #ffffffff > color (#!3#!4.1 & sel) #c0c0c0ff > color (#!3#!4.1 & sel) #d6d6d6ff > select Fe 66 atoms, 66 residues, 11 models selected > color (#!3#!4.1 & sel) #5e5e5eff > color (#!3#!4.1 & sel) #424242ff > color (#!3#!4.1 & sel) #212121ff > select clear > select #1-6/A-F:40 1356 atoms, 1290 bonds, 66 residues, 11 models selected > color (#!3#!4.1 & sel) purple > color (#!3#!4.1 & sel) #ff40ffff > color (#!3#!4.1 & sel) #ff85ffff > color (#!3#!4.1 & sel) #ff8ad8ff > color (#!3#!4.1 & sel) #ff2f92ff > color (#!3#!4.1 & sel) #fffb00ff > color (#!3#!4.1 & sel) #fffc79ff > color (#!3#!4.1 & sel) #ffd479ff > color (#!3#!4.1 & sel) #ffe178ff > color (#!3#!4.1 & sel) #ffe96aff > color (#!3#!4.1 & sel) #ffeb68ff > color (#!3#!4.1 & sel) #ffeb67ff > color (#!3#!4.1 & sel) #ffed63ff > color (#!3#!4.1 & sel) #ffed62ff > color (#!3#!4.1 & sel) #ffee61ff > color (#!3#!4.1 & sel) #ffef5fff > color (#!3#!4.1 & sel) #fff05eff > color (#!3#!4.1 & sel) #fff05fff > color (#!3#!4.1 & sel) #ffe667ff > color (#!3#!4.1 & sel) #ffe36aff > color (#!3#!4.1 & sel) #ffe26aff > color (#!3#!4.1 & sel) #ffdd6fff > color (#!3#!4.1 & sel) #ffdc70ff > color (#!3#!4.1 & sel) #ffdb70ff > color (#!3#!4.1 & sel) #ffd971ff > color (#!3#!4.1 & sel) #ffd870ff > color (#!3#!4.1 & sel) #ffd76eff > color (#!3#!4.1 & sel) #ffd76cff > color (#!3#!4.1 & sel) #ffd66bff > color (#!3#!4.1 & sel) #ffd267ff > color (#!3#!4.1 & sel) #ffcf64ff > color (#!3#!4.1 & sel) #ffcf63ff > color (#!3#!4.1 & sel) #ffd064ff > color (#!3#!4.1 & sel) #ffd065ff > color (#!3#!4.1 & sel) #ffd165ff > color (#!3#!4.1 & sel) #ffd166ff > color (#!3#!4.1 & sel) #deb658ff > color (#!3#!4.1 & sel) #c9a550ff > color (#!3#!4.1 & sel) #bf9d4cff > color (#!3#!4.1 & sel) #a88a43ff > color (#!3#!4.1 & sel) #9b7f3eff > color (#!3#!4.1 & sel) #ad8e45ff > color (#!3#!4.1 & sel) #b9984aff > color (#!3#!4.1 & sel) #e5bc5bff > color (#!3#!4.1 & sel) #e9bf5dff > color (#!3#!4.1 & sel) #eac05dff > color (#!3#!4.1 & sel) #eec45fff > color (#!3#!4.1 & sel) #f4c961ff > color (#!3#!4.1 & sel) #f5c962ff > color (#!3#!4.1 & sel) #ffd166ff > color (#!3#!4.1 & sel) #ffe35eff > color (#!3#!4.1 & sel) #ffed54ff > color (#!3#!4.1 & sel) #ffea5aff > color (#!3#!4.1 & sel) #ffe75dff > color (#!3#!4.1 & sel) #ffe65fff > color (#!3#!4.1 & sel) #ffe461ff > color (#!3#!4.1 & sel) #ffe364ff > color (#!3#!4.1 & sel) #ffe167ff > color (#!3#!4.1 & sel) #ffda71ff > color (#!3#!4.1 & sel) #ffd872ff > color (#!3#!4.1 & sel) #ffd572ff > color (#!3#!4.1 & sel) #ffd479ff > select clear > select #1-6/A-F:47 1182 atoms, 1116 bonds, 66 residues, 11 models selected > color (#!3#!4.1 & sel) #ffd479ff > select clear > hide H > save > /Users/anushkaghosh/Documents/Documents/chimaera/DTHP_double_mutants/Q47KK40T-full.png > width 1329 height 782 supersample 3 transparentBackground true > view > select #1-6/A-F:40,47 2538 atoms, 2406 bonds, 132 residues, 11 models selected > view sel > hide #* target a > show (#!3#!4.1 & sel) target ab > label (#!3#!4.1 & sel) text ""{0.name} {0.number}{0.insertion_code}"" > hide H > select clear > select #4.1/B:47@NZ 1 atom, 1 residue, 1 model selected > select add #3/A:40@OG1 2 atoms, 2 residues, 2 models selected > ui tool show H-Bonds > hbonds sel color #ff202d restrict cross interModel false intraModel false > intraMol false intraRes false reveal true 0 hydrogen bonds found > hbonds sel color #ff202d restrict cross interModel false intraModel false > intraMol false intraRes false reveal true 0 hydrogen bonds found > hbonds sel color #ff202d restrict cross reveal true 2 hydrogen bonds found > show hbonds > ui tool show ""Check Waters"" > hbonds #3/S:2-674 interModel false reveal true restrict any name ""water > H-bonds"" 332 hydrogen bonds found > select #3/S:2-674 119 atoms, 178 pseudobonds, 119 residues, 2 models selected > display #3/S:2-674 : view #3/S:2-674 @ hide hbonds No waters chosen > delete Missing or invalid ""atoms"" argument: empty atom specifier > hide > select #1-6/A-F:40,47 2538 atoms, 2406 bonds, 132 residues, 11 models selected > show sel & #!3#!4.1 atoms > hide > show sel & #!3#!4.1 atoms > hide H > select clear > select #4.1/D:47@NZ 1 atom, 1 residue, 1 model selected > select #3/D:40@OG1 1 atom, 1 residue, 1 model selected > select add #4.1/D:47@NZ 2 atoms, 2 residues, 2 models selected > ui tool show Contacts > contacts sel restrict both ignoreHiddenModels true select true No contacts > select #3/D:40@OG1 1 atom, 1 residue, 1 model selected > select add #4.1/D:47@NZ 2 atoms, 2 residues, 2 models selected > ui tool show Distances > distance #3/D:40@OG1 #4.1/D:47@NZ Distance between DTHP_K40TQ47K_refine_026-coot-0.pdb #3/D THR 40 OG1 and DTHP_K40TQ47K_refine_026-coot-0.pdb 0 0 0 sym 1 #4.1/D LYS 47 NZ: 3.13Å > select clear > select #3/E:47@NZ 1 atom, 1 residue, 1 model selected > select add #4.1/C:40@CG2 2 atoms, 2 residues, 2 models selected > distance #3/E:47@NZ #4.1/C:40@CG2 Distance between DTHP_K40TQ47K_refine_026-coot-0.pdb #3/E LYS 47 NZ and DTHP_K40TQ47K_refine_026-coot-0.pdb 0 0 0 sym 1 #4.1/C THR 40 CG2: 9.36Å > select clear > save > /Users/anushkaghosh/Documents/Documents/chimaera/DTHP_double_mutants/Q47KK40T-close.png > width 1329 height 782 supersample 3 transparentBackground true > ui windowfill toggle > open /Users/anushkaghosh/Downloads/HTHP_bessy200319_C2221.pdb format pdb Chain information for HTHP_bessy200319_C2221.pdb #10 --- Chain | Description A B E | No description available C D F | No description available 64 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open /Users/anushkaghosh/Downloads/HTHP_bessy200319_C2221.pdb format pdb Chain information for HTHP_bessy200319_C2221.pdb #11 --- Chain | Description A B E | No description available C D F | No description available 64 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > show #!3,10-11#!4.1 cartoons Computing secondary structure > style #!3,10-11#!4.1 stick Changed 30368 atom styles > hide #!3,10-11#!4.1 atoms > volume style surface No volumes specified > volume style mesh No volumes specified > view clip false > save > /Users/anushkaghosh/Documents/Documents/chimaera/DTHP_double_mutants/bleh.cxs > hide #!4 models > hide #!3 models > hide #7 models > hide #8 models > select subtract #8 Nothing selected > hide #!9 models > hide #9.1 models > ui tool show ""Crystal Contacts"" > crystalcontacts #10 distance 1 1 pairs of asymmetric units of HTHP_bessy200319_C2221.pdb contact at distance 1.0 A Atoms MTRIX SMTRY Unit cell MTRIXref Copies 2 0 2 0 0 -1 0 1 > select ::name=""HEM"" 5694 atoms, 5928 bonds, 312 pseudobonds, 78 residues, 26 models selected > show sel & #!10-11#!2.1 atoms > select clear > select #10/A:43 10 atoms, 9 bonds, 1 residue, 1 model selected > select #10-11/A-F:40,47 468 atoms, 444 bonds, 24 residues, 2 models selected > select #10,11/A-F:40,47 468 atoms, 444 bonds, 24 residues, 2 models selected > crystalcontacts delete #10 > crystalcontacts #10 distance 1 rainbow false 1 pairs of asymmetric units of HTHP_bessy200319_C2221.pdb contact at distance 1.0 A Atoms MTRIX SMTRY Unit cell MTRIXref Copies 2 0 2 0 0 -1 0 1 > select clear > save > /Users/anushkaghosh/Documents/Documents/chimaera/DTHP_double_mutants/bleh.cxs ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M1 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: Mac mini Model Identifier: Macmini9,1 Model Number: Z12N0006DD/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6.1 (24G90) Kernel Version: Darwin 24.6.0 Time since boot: 3 days, 8 hours, 40 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: DELL U2720Q: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 50.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported 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