id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17912 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.0-arm64-arm-64bit ChimeraX Version: 1.9.dev202406122300 (2024-06-12 23:00:04 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=5.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=5.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1920K 15 \nActivity Tracing 256K 1 \nCG backing stores 960K 4 \nCG image 288K 16 \nColorSync 640K 29 \nCoreAnimation 192K 12 \nCoreGraphics 48K 3 \nCoreUI image data 1728K 26 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 4.0G 610 \nMALLOC guard page 192K 11 \nMALLOC_MEDIUM (reserved) 512.0M 7 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 688K 43 \nStack 173.0M 44 \nStack Guard 56.0M 1 \nVM_ALLOCATE 374.3M 555 \nVM_ALLOCATE (reserved) 160.0M 3 reserved VM address space (unallocated)\n__AUTH 1938K 369 \n__AUTH_CONST 25.0M 600 \n__CTF 756 1 \n__DATA 20.6M 754 \n__DATA_CONST 38.7M 758 \n__DATA_DIRTY 2030K 238 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 791.8M 158 \n__OBJC_CONST 4847K 337 \n__OBJC_RO 65.1M 1 \n__OBJC_RW 1981K 1 \n__TEXT 842.0M 780 \ndyld private memory 304K 2 \nmapped file 212.8M 60 \nshared memory 3168K 25 \n=========== ======= ======= \nTOTAL 7.3G 5477 \nTOTAL, minus reserved VM space 6.6G 5477 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""63582c5f8a53461413999550"", ""factorPackIds"" : { ""PROACTIVE_MAIL_INTELLIGENCE_SALIENCY"" : ""636525247ea6e25a76dc2008"" }, ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 } ], ""experiments"" : [ ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== UCSF ChimeraX version: 1.9.dev202406122300 (2024-06-12) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/uijin/Desktop/GTR1_Map and Models/Pontus > Gourdon/GTR1_apo_IF_8.0/Gtr1_apo.pdb"" format pdb Chain information for Gtr1_apo.pdb #1 --- Chain | Description A | No description available > open ""/Users/uijin/Desktop/GTR1_Map and > Models/GTR1I_6.0_IF/GTR1I_6.0_IF.pdb"" format pdb Chain information for GTR1I_6.0_IF.pdb #2 --- Chain | Description B | No description available > open ""/Users/uijin/Library/Mobile Documents/com~apple~CloudDocs/Lab > Archive/Project/GTR1 (2024.02~)/Map and > Models/GTR1M_6.0_OCC_full/GTR1M_6.0_OCC_full_pre-model.pdb"" format pdb Chain information for GTR1M_6.0_OCC_full_pre-model.pdb #3 --- Chain | Description B | No description available > matchmaker #3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GTR1I_6.0_IF.pdb, chain B (#2) with GTR1M_6.0_OCC_full_pre- model.pdb, chain B (#3), sequence alignment score = 2627.4 RMSD between 446 pruned atom pairs is 0.924 angstroms; (across all 532 pairs: 2.099) > close #1 > open ""/Users/uijin/Library/Mobile Documents/com~apple~CloudDocs/Lab > Archive/Project/GTR1 (2024.02~)/Map and > Models/GTR1A_OCC_7.5_V/GTR1A_OCC_7.5.pdb"" format pdb Chain information for GTR1A_OCC_7.5.pdb #1 --- Chain | Description A | No description available > matchmaker #1 to #3 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 GTR1M_6.0_OCC_full_pre-model.pdb, chain B (#3) with GTR1A_OCC_7.5.pdb, chain A (#1), sequence alignment score = 2618.5 RMSD between 319 pruned atom pairs is 0.948 angstroms; (across all 527 pairs: 3.080) > hide #!1 models > show #!1 models > hide #2 models > rename #3 id #2 > show #!2 models > hide #!2 target m > close #2 > open ""/Users/uijin/Library/Mobile Documents/com~apple~CloudDocs/Lab > Archive/Project/GTR1 (2024.02~)/Map and > Models/GTR1M_6.0_OCC_full/GTR1M_6.0_OCC_full_pre-model.pdb"" format pdb Chain information for GTR1M_6.0_OCC_full_pre-model.pdb #2 --- Chain | Description B | No description available > open ""/Users/uijin/Desktop/GTR1_Map and > Models/GTR1I_6.0_IF/GTR1I_6.0_IF.pdb"" format pdb Chain information for GTR1I_6.0_IF.pdb #3 --- Chain | Description B | No description available > 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 GTR1A_OCC_7.5.pdb, chain A (#1) with GTR1M_6.0_OCC_full_pre- model.pdb, chain B (#2), sequence alignment score = 2618.5 RMSD between 319 pruned atom pairs is 0.948 angstroms; (across all 527 pairs: 3.080) Matchmaker GTR1A_OCC_7.5.pdb, chain A (#1) with GTR1I_6.0_IF.pdb, chain B (#3), sequence alignment score = 2679.5 RMSD between 279 pruned atom pairs is 0.797 angstroms; (across all 531 pairs: 4.416) > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #3 models > hide #!2 models > show #!2 models > rainbow > show #3 models > hide #!2 models > hide #!1 models > show #!2 models > show #!1 models > open ""/Users/uijin/Library/Mobile Documents/com~apple~CloudDocs/Lab > Archive/Project/GTR1 (2024.02~)/Map and Models/Pontus > Gourdon/GTR3_I3M_IF_6.5 /Gtr3_pH6.5.pdb"" Chain information for Gtr3_pH6.5.pdb #4 --- Chain | Description A | No description available > matchmaker #4 to #3 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 GTR1I_6.0_IF.pdb, chain B (#3) with Gtr3_pH6.5.pdb, chain A (#4), sequence alignment score = 2117.8 RMSD between 470 pruned atom pairs is 0.967 angstroms; (across all 540 pairs: 1.885) > rainbow > hide #!1 models > hide #!2 models > show atoms > color byhetero > hide #250-1000 atoms > hide :300-1000 atoms > hide H > show atoms > hide H > open ""/Users/uijin/Library/Mobile Documents/com~apple~CloudDocs/Lab > Archive/Project/GTR1 (2024.02~)/Map and Models/Pontus > Gourdon/GTR3_apo_OCC_8.0 /Gtr3_apo.pdb"" Chain information for Gtr3_apo.pdb #5 --- Chain | Description A | No description available > matchmaker #5 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GTR1A_OCC_7.5.pdb, chain A (#1) with Gtr3_apo.pdb, chain A (#5), sequence alignment score = 1812.2 RMSD between 335 pruned atom pairs is 1.106 angstroms; (across all 489 pairs: 2.702) > rainbow > show atoms > hide H > color byhetero > hide #3 models > hide #!4 models > show #!1 models > hide #!5 models > hide atoms > show :513 atoms > show #!2 models > show #3 models > hide H > hide #3 models > show #3 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > select :513 48 atoms, 43 bonds, 5 residues, 5 models selected > hbonds sel & #3#!1-2 reveal true 57 hydrogen bonds found > select clear > hide #!1 models > show #!1 models > hide #!2 models > show #!2 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 #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 #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > open /Users/uijin/Downloads/cryosparc_P3_J2119_008_volume_map_sharp.mrc Opened cryosparc_P3_J2119_008_volume_map_sharp.mrc as #7, grid size 240,240,240, pixel 0.901, shown at level 0.0468, step 1, values float32 > hide #!1 models > hide #!2 models > hide #3 models > hide #6 models > volume #7 level 0.1567 > open ""/Users/uijin/Library/Mobile Documents/com~apple~CloudDocs/Lab > Archive/Project/GTR1 (2024.02~)/Map and > Models/Updates_Jan2025/GTR1_apo_6.0_Jan2025.pdb"" Chain information for GTR1_apo_6.0_Jan2025.pdb #8 --- Chain | Description A | No description available > ui tool show ""Fit in Map"" > fitmap #8 inMap #7 Fit molecule GTR1_apo_6.0_Jan2025.pdb (#8) to map cryosparc_P3_J2119_008_volume_map_sharp.mrc (#7) using 4105 atoms average map value = 0.1642, steps = 108 shifted from previous position = 1.84 rotated from previous position = 11.6 degrees atoms outside contour = 2129, contour level = 0.15666 Position of GTR1_apo_6.0_Jan2025.pdb (#8) relative to cryosparc_P3_J2119_008_volume_map_sharp.mrc (#7) coordinates: Matrix rotation and translation 0.99211889 0.09596544 -0.08056509 -1.71671143 -0.10749464 0.98224775 -0.15373439 31.01798183 0.06438169 0.16118311 0.98482232 -23.37018498 Axis 0.78343842 -0.36059247 -0.50615938 Axis point 0.00000000 164.25022773 181.15325648 Rotation angle (degrees) 11.59451868 Shift along axis -0.70075007 > save 2119.pdb #8 > open /Users/uijin/Downloads/cryosparc_P3_J2128_007_volume_map_sharp.mrc Opened cryosparc_P3_J2128_007_volume_map_sharp.mrc as #9, grid size 240,240,240, pixel 0.901, shown at level 0.0481, step 1, values float32 > hide #!7 models > volume #9 level 0.1991 > select add #8 4105 atoms, 4213 bonds, 1 pseudobond, 522 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.90352,-0.42705,-0.035751,250.27,0.40729,-0.88166,0.23832,124.26,-0.13329,0.20076,0.97053,-4.6786 > fitmap #8 inMap #9 Fit molecule GTR1_apo_6.0_Jan2025.pdb (#8) to map cryosparc_P3_J2128_007_volume_map_sharp.mrc (#9) using 4105 atoms average map value = 0.0485, steps = 108 shifted from previous position = 3.55 rotated from previous position = 3.99 degrees atoms outside contour = 3481, contour level = 0.19908 Position of GTR1_apo_6.0_Jan2025.pdb (#8) relative to cryosparc_P3_J2128_007_volume_map_sharp.mrc (#9) coordinates: Matrix rotation and translation -0.87673545 -0.48056076 -0.01990761 253.58996440 0.46640071 -0.85955529 0.20889013 120.88438925 -0.11749609 0.17385645 0.97773647 -2.50031376 Axis -0.03677608 0.10244208 0.99405892 Axis point 111.34532317 92.90248942 0.00000000 Rotation angle (degrees) 151.55528712 Shift along axis 0.57214246 > view matrix models > #8,-0.9716,-0.2366,0.0031723,236.23,0.23529,-0.96464,0.11875,166.26,-0.025035,0.11612,0.99292,-8.1467 > fitmap #8 inMap #9 Fit molecule GTR1_apo_6.0_Jan2025.pdb (#8) to map cryosparc_P3_J2128_007_volume_map_sharp.mrc (#9) using 4105 atoms average map value = 0.08762, steps = 88 shifted from previous position = 5.96 rotated from previous position = 10.4 degrees atoms outside contour = 3174, contour level = 0.19908 Position of GTR1_apo_6.0_Jan2025.pdb (#8) relative to cryosparc_P3_J2128_007_volume_map_sharp.mrc (#9) coordinates: Matrix rotation and translation -0.99500932 -0.08273165 -0.05578467 226.80069626 0.07110080 -0.98009858 0.18534145 183.16152629 -0.07000808 0.18045014 0.98108950 -11.41175418 Axis -0.03164547 0.09202158 0.99525403 Axis point 109.65489745 96.51674693 0.00000000 Rotation angle (degrees) 175.56759009 Shift along axis -1.67999608 > view matrix models > #8,-0.9433,-0.33186,-0.0070666,241.5,0.33128,-0.93988,-0.08287,180.35,0.02086,-0.080512,0.99654,3.9235 > fitmap #8 inMap #9 Fit molecule GTR1_apo_6.0_Jan2025.pdb (#8) to map cryosparc_P3_J2128_007_volume_map_sharp.mrc (#9) using 4105 atoms average map value = 0.2092, steps = 128 shifted from previous position = 6.21 rotated from previous position = 19.3 degrees atoms outside contour = 2170, contour level = 0.19908 Position of GTR1_apo_6.0_Jan2025.pdb (#8) relative to cryosparc_P3_J2128_007_volume_map_sharp.mrc (#9) coordinates: Matrix rotation and translation -0.99736419 -0.06329504 -0.03547412 227.44034456 0.05928203 -0.99274712 0.10458872 196.60738048 -0.04183677 0.10221006 0.99388268 -6.35153927 Axis -0.01937564 0.05182788 0.99846805 Axis point 110.63355249 101.96724162 0.00000000 Rotation angle (degrees) 176.48082563 Shift along axis -0.55886767 > fitmap #8 inMap #9 Fit molecule GTR1_apo_6.0_Jan2025.pdb (#8) to map cryosparc_P3_J2128_007_volume_map_sharp.mrc (#9) using 4105 atoms average map value = 0.2092, steps = 28 shifted from previous position = 0.0213 rotated from previous position = 0.0115 degrees atoms outside contour = 2172, contour level = 0.19908 Position of GTR1_apo_6.0_Jan2025.pdb (#8) relative to cryosparc_P3_J2128_007_volume_map_sharp.mrc (#9) coordinates: Matrix rotation and translation -0.99736364 -0.06320680 -0.03564636 227.43030336 0.05917890 -0.99275909 0.10453345 196.61889004 -0.04199547 0.10214835 0.99388233 -6.33353919 Axis -0.01945853 0.05179842 0.99846797 Axis point 110.63299349 101.96680718 0.00000000 Rotation angle (degrees) 176.48632640 Shift along axis -0.56474702 > save 2128.pdb #8 > close #8-9 > show #!7 models > close #7 > show #6 models > show #!1 models > hide #6 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > open ""/Users/uijin/Library/Mobile Documents/com~apple~CloudDocs/Lab > Archive/Project/GTR1 (2024.02~)/Map and > Models/Updates_Jan2025/GTR1_apo_6.0_Jan2025.pdb"" Chain information for GTR1_apo_6.0_Jan2025.pdb #7 --- Chain | Description A | No description available > matchmaker #7 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GTR1M_6.0_OCC_full_pre-model.pdb, chain B (#2) with GTR1_apo_6.0_Jan2025.pdb, chain A (#7), sequence alignment score = 2510 RMSD between 274 pruned atom pairs is 0.994 angstroms; (across all 514 pairs: 4.408) > rainbow > 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 > show #!2 models > morph #7 #2 Computed 51 frame morph #8 > coordset #8 1,51 > rainbow > show #1-100 atoms > ubdo Unknown command: ubdo > ubdo Unknown command: ubdo > undo > show :1-100 atoms > color byhetero > select #8:1-100 atoms Expected a keyword > select #8:1-100 289 atoms, 295 bonds, 36 residues, 1 model selected > hbonds sel reveal true 209 hydrogen bonds found > show #6 models > select clear > show :196 atoms > hide #6 models > show #6 models > show #3 models > hide H > morph #8 #2 #3 Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/morph.py"", line 84, in morph traj = compute_morph(structures, session.logger, method=method, rate=rate, frames=frames, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/motion.py"", line 28, in compute_morph motion.interpolate(res_groups, atom_map, res_interp) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/motion.py"", line 149, in interpolate coords0[maindices] = matoms.coords ~~~~~~~^^^^^^^^^^^ IndexError: index 4031 is out of bounds for axis 0 with size 4031 IndexError: index 4031 is out of bounds for axis 0 with size 4031 File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/motion.py"", line 149, in interpolate coords0[maindices] = matoms.coords ~~~~~~~^^^^^^^^^^^ See log for complete Python traceback. > hide #3 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > show #!7 models > hide #!7 models > morph #7 #2 #3 Computed 101 frame morph #9 > coordset #9 1,101 > hide #!8 models > rainbow > show :196 atoms > show :1-100 atoms > color byhetero > select :1-100 3293 atoms, 3362 bonds, 151 pseudobonds, 400 residues, 9 models selected > hbonds sel & #!9 reveal true 230 hydrogen bonds found > select clear > morph #7 #3 Computed 51 frame morph #10 > coordset #10 1,51 > hide #!9 models > color byhetero > rainbow > color byhetero > select :1-100 3624 atoms, 3700 bonds, 166 pseudobonds, 441 residues, 10 models selected > hbonds sel & #!10 reveal true 299 hydrogen bonds found > select clear > select :86 78 atoms, 69 bonds, 9 residues, 9 models selected > interfaces select & #!10 & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > interfaces select & #!10 & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select clear > show :111 > show :115 > hide #!10 models > show #!9 models > open 7nqk Summary of feedback from opening 7nqk fetched from pdb --- note | Fetching compressed mmCIF 7nqk from http://files.rcsb.org/download/7nqk.cif 7nqk title: Cryo-EM structure of the mammalian peptide transporter PepT2 [more info...] Chain information for 7nqk #11 --- Chain | Description | UniProt A | Solute carrier family 15 member 2 | S15A2_RAT 1-729 B | nanobody | > matchmaker #11 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GTR1A_OCC_7.5.pdb, chain A (#1) with 7nqk, chain A (#11), sequence alignment score = 600.4 RMSD between 209 pruned atom pairs is 1.228 angstroms; (across all 466 pairs: 7.209) > rainbow > hide #!9 models > show #!1 models > hide #!1 models > show #11:87 atoms > open 2xut Summary of feedback from opening 2xut fetched from pdb --- note | Fetching compressed mmCIF 2xut from http://files.rcsb.org/download/2xut.cif 2xut title: Crystal structure of a proton dependent oligopeptide (POT) family transporter. [more info...] Chain information for 2xut #12 --- Chain | Description | UniProt A B C | PROTON/PEPTIDE SYMPORTER FAMILY PROTEIN | Q8EKT7_SHEON 1-516 2xut mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly > matchmaker #12 to #11 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 7nqk, chain A (#11) with 2xut, chain B (#12), sequence alignment score = 651.5 RMSD between 124 pruned atom pairs is 0.978 angstroms; (across all 408 pairs: 11.501) > rainbow > hide #11 models > show #11 models > hide #!12 models > show #!12 models > hide #11 models > show #12:61 atoms > coulombic #!12 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 2xut_A SES surface #12.2: minimum, -15.80, mean 0.12, maximum 15.66 Coulombic values for 2xut_B SES surface #12.3: minimum, -15.98, mean 0.10, maximum 14.99 Coulombic values for 2xut_C SES surface #12.4: minimum, -15.69, mean 0.13, maximum 15.76 To also show corresponding color key, enter the above coulombic command and add key true > view > ui tool show ""Side View"" > delete #12/A/B > hide #!12 surfaces > show #12:61 atoms > show #!12 surfaces > hide #!12 surfaces > show #!12 surfaces > hide #!12 surfaces > show #!12 surfaces > close #12 > show #11 models > hide #11 models > show #!9 models > color byhetero ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.9.dev202406122300 (2024-06-12) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: Z11C001DKKH/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8419.41.10 OS Loader Version: 8419.41.10 Software: System Software Overview: System Version: macOS 13.0 (22A380) Kernel Version: Darwin 22.1.0 Time since boot: 22 days, 6 hours, 22 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: LS32A600U: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 75.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.13 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.2 ChimeraX-AtomicLibrary: 14.1.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 2.2.4 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.dev202406122300 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-DeepMutationalScan: 1.0 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.4 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 3.1.5 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.12.1 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.6 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 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: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.32.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX