id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17387 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.4-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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""com.apple.Foundation"", ""size"" : 14676544, ""uuid"" : ""5ab66e9b-19c0-3fe8-9793-d5156d1c7050"", ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"", ""name"" : ""Foundation"", ""CFBundleVersion"" : ""3423"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6884990976, ""CFBundleShortVersionString"" : ""1.22"", ""CFBundleIdentifier"" : ""com.apple.HIServices"", ""size"" : 443264, ""uuid"" : ""fcb9ea71-5118-331b-9070-ba311437eafb"", ""path"" : ""\/System\/Library\/Frameworks\/ApplicationServices.framework\/Versions\/A\/Frameworks\/HIServices.framework\/Versions\/A\/HIServices"", ""name"" : ""HIServices"" } ], ""sharedCache"" : { ""base"" : 6767673344, ""size"" : 5020090368, ""uuid"" : ""32a9f5fd-14a8-3423-8952-1464a6903997"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=27.8G written=31.3M(0%) resident=14.1M(0%) swapped_out=17.3M(0%) unallocated=27.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 1376K 66 \nColorSync 656K 33 \nCoreAnimation 2080K 123 \nCoreGraphics 96K 6 \nCoreServices 624K 2 \nCoreUI image data 5616K 56 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 27.0G 196 \nMALLOC guard page 288K 18 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.5M 32 \nStack 189.1M 32 \nVM_ALLOCATE 291.1M 263 \nVM_ALLOCATE (reserved) 288.0M 2 reserved VM address space (unallocated)\n__AUTH 5487K 696 \n__AUTH_CONST 77.2M 943 \n__CTF 824 1 \n__DATA 34.4M 1098 \n__DATA_CONST 37.1M 1114 \n__DATA_DIRTY 2775K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 652.9M 166 \n__OBJC_RO 61.3M 1 \n__OBJC_RW 2391K 1 \n__TEXT 1.3G 1133 \n__TEXT (graphics) 400K 1 \n__TPRO_CONST 128K 2 \ndyld private memory 4384K 36 \nmapped file 606.7M 102 \npage table in kernel 14.1M 1 \nshared memory 3712K 25 \n=========== ======= ======= \nTOTAL 30.6G 6507 \nTOTAL, minus reserved VM space 30.3G 6507 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""e775d15267c64573543e38aa8001f9fd0fae3adc"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""64628732bf2f5257dedc8988"", ""factorPackIds"" : { }, ""deploymentId"" : 240000001 }, { ""rolloutId"" : ""652eff3d1bce5442b8d753c9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000009 } ], ""experiments"" : [ { ""treatmentId"" : ""28060e10-d4e5-4163-aa2b-d8bd088d5cbf"", ""experimentId"" : ""6685b283afc7c17197d69eec"", ""deploymentId"" : 400000007 }, { ""treatmentId"" : ""d7ff00dd-1c5a-4dbb-85d6-7a936d671384"", ""experimentId"" : ""67f46bbc84eaf455d73c6098"", ""deploymentId"" : 400000001 } ] } } ===== Log before crash start ===== 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 > open > /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_7ZA1_mono.pdb > open > /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_7ZA1_mono.pdb > format pdb > open > /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft_monomer.pdb > open /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/UNC5D_5fft.pdb Chain information for UNC5D_5fft.pdb #1 --- Chain | Description A E | No description available B F | No description available C D G H | No description available > show atoms > show cartoons > hide atoms > close session > open > /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft.pdb Summary of feedback from opening /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 91 HIS A 95 1 5 Start residue of secondary structure not found: HELIX 2 2 THR A 117 ASP A 123 1 7 Start residue of secondary structure not found: HELIX 3 3 ALA B 82 VAL B 87 1 6 Start residue of secondary structure not found: HELIX 4 4 SER B 125 LEU B 132 1 8 Start residue of secondary structure not found: HELIX 5 5 ALA B 154 ALA B 158 1 5 26 messages similar to the above omitted End residue of secondary structure not found: SHEET 4 4 1 GLN A 80 CYS A 85 0 End residue of secondary structure not found: SHEET 5 5 1 GLU A 88 TRP A 89 0 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 96 GLU A 98 0 Start residue of secondary structure not found: SHEET 7 7 1 ARG A 110 PHE A 113 0 Start residue of secondary structure not found: SHEET 8 8 1 TRP A 131 TRP A 137 0 Start residue of secondary structure not found: SHEET 9 9 1 THR A 142 LYS A 144 0 Start residue of secondary structure not found: SHEET 10 10 1 ALA A 148 SER A 149 0 161 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (73 ) Cannot find LINK/SSBOND residue CYS (85 ) Cannot find LINK/SSBOND residue CYS (178 ) Cannot find LINK/SSBOND residue CYS (262 ) Cannot find LINK/SSBOND residue CYS (266 ) 69 messages similar to the above omitted Chain information for modeller_UNC5D_5fft.pdb #1 --- Chain | Description A E | No description available Computing secondary structure > close > open > /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_7ZA1.pdb Summary of feedback from opening /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_7ZA1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 91 HIS A 95 1 5 Start residue of secondary structure not found: HELIX 2 2 THR A 117 ASP A 123 1 7 Start residue of secondary structure not found: HELIX 3 3 ALA B 82 VAL B 87 1 6 Start residue of secondary structure not found: HELIX 4 4 SER B 125 LEU B 132 1 8 Start residue of secondary structure not found: HELIX 5 5 ALA B 154 ALA B 158 1 5 26 messages similar to the above omitted End residue of secondary structure not found: SHEET 4 4 1 GLN A 80 CYS A 85 0 End residue of secondary structure not found: SHEET 5 5 1 GLU A 88 TRP A 89 0 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 96 GLU A 98 0 Start residue of secondary structure not found: SHEET 7 7 1 ARG A 110 PHE A 113 0 Start residue of secondary structure not found: SHEET 8 8 1 TRP A 131 TRP A 137 0 Start residue of secondary structure not found: SHEET 9 9 1 THR A 142 LYS A 144 0 Start residue of secondary structure not found: SHEET 10 10 1 ALA A 148 SER A 149 0 161 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (73 ) Cannot find LINK/SSBOND residue CYS (85 ) Cannot find LINK/SSBOND residue CYS (178 ) Cannot find LINK/SSBOND residue CYS (262 ) Cannot find LINK/SSBOND residue CYS (266 ) 69 messages similar to the above omitted Start residue of secondary structure not found: HELIX 1 1 HIS A 91 HIS A 95 1 5 Start residue of secondary structure not found: HELIX 2 2 THR A 117 ASP A 123 1 7 Start residue of secondary structure not found: HELIX 3 3 ALA B 82 VAL B 87 1 6 Start residue of secondary structure not found: HELIX 4 4 SER B 125 LEU B 132 1 8 Start residue of secondary structure not found: HELIX 5 5 ALA B 154 ALA B 158 1 5 111 messages similar to the above omitted End residue of secondary structure not found: SHEET 89 89 1 GLN E 80 CYS E 85 0 End residue of secondary structure not found: SHEET 90 90 1 GLU E 88 TRP E 89 0 Start residue of secondary structure not found: SHEET 91 91 1 VAL E 96 LEU E 101 0 Start residue of secondary structure not found: SHEET 92 92 1 LYS E 108 ILE E 114 0 Start residue of secondary structure not found: SHEET 93 93 1 TRP E 131 TRP E 137 0 Start residue of secondary structure not found: SHEET 94 94 1 THR E 142 LYS E 144 0 Start residue of secondary structure not found: SHEET 95 95 1 ALA E 148 SER E 149 0 24 messages similar to the above omitted End residue of secondary structure not found: SHEET 120 120 1 ARG F 280 ASP F 282 0 Start residue of secondary structure not found: SHEET 121 121 1 GLN F 304 THR F 306 0 Start residue of secondary structure not found: SHEET 122 122 1 TRP F 312 PHE F 313 0 Start residue of secondary structure not found: SHEET 123 123 1 ASN F 333 ARG F 335 0 Start residue of secondary structure not found: SHEET 124 124 1 CYS F 339 GLY F 341 0 Start residue of secondary structure not found: SHEET 125 125 1 ARG G 99 CYS G 104 0 46 messages similar to the above omitted Chain information for modeller_UNC5D_7ZA1.pdb --- Chain | Description 1.1/A 1.1/E 1.2/E 1.2/F 1.2/G 1.2/H | No description available Computing secondary structure > hide #1.2 models > close #1.2 > select add #1.1 6574 atoms, 6658 bonds, 420 residues, 1 model selected > select subtract #1.1 Nothing selected > Selecty /A Unknown command: Selecty /A > Selecty #1/A Unknown command: Selecty #1/A > Select #1/A Unknown command: Select #1/A > Select #1/A Unknown command: Select #1/A > Select #/A Unknown command: Select #/A > Select /A Unknown command: Select /A > Select #1.1/A Unknown command: Select #1.1/A > select /A 3287 atoms, 3329 bonds, 210 residues, 1 model selected > select /E 3287 atoms, 3329 bonds, 210 residues, 1 model selected > delete atoms sel > delete bonds sel > select /A 3287 atoms, 3329 bonds, 210 residues, 1 model selected > save > /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_7ZA1_monomer.pdb > close session > open > /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_7ZA1_monomer.pdb > format pdb Chain information for modeller_UNC5D_7ZA1_monomer.pdb #1 --- Chain | Description A | No description available > open > /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft_monomer.pdb > select add #1 3287 atoms, 3329 bonds, 210 residues, 1 model selected > select subtract #1 Nothing selected > close session > open > /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft_monomer.pdb > open > /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft.pdb Summary of feedback from opening /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 91 HIS A 95 1 5 Start residue of secondary structure not found: HELIX 2 2 THR A 117 ASP A 123 1 7 Start residue of secondary structure not found: HELIX 3 3 ALA B 82 VAL B 87 1 6 Start residue of secondary structure not found: HELIX 4 4 SER B 125 LEU B 132 1 8 Start residue of secondary structure not found: HELIX 5 5 ALA B 154 ALA B 158 1 5 26 messages similar to the above omitted End residue of secondary structure not found: SHEET 4 4 1 GLN A 80 CYS A 85 0 End residue of secondary structure not found: SHEET 5 5 1 GLU A 88 TRP A 89 0 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 96 GLU A 98 0 Start residue of secondary structure not found: SHEET 7 7 1 ARG A 110 PHE A 113 0 Start residue of secondary structure not found: SHEET 8 8 1 TRP A 131 TRP A 137 0 Start residue of secondary structure not found: SHEET 9 9 1 THR A 142 LYS A 144 0 Start residue of secondary structure not found: SHEET 10 10 1 ALA A 148 SER A 149 0 161 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (73 ) Cannot find LINK/SSBOND residue CYS (85 ) Cannot find LINK/SSBOND residue CYS (178 ) Cannot find LINK/SSBOND residue CYS (262 ) Cannot find LINK/SSBOND residue CYS (266 ) 69 messages similar to the above omitted Chain information for modeller_UNC5D_5fft.pdb #1 --- Chain | Description A E | No description available Computing secondary structure > select /E 3287 atoms, 3329 bonds, 210 residues, 1 model selected > select /A 3287 atoms, 3329 bonds, 210 residues, 1 model selected > delete atoms sel > delete bonds sel > select /E 3287 atoms, 3329 bonds, 210 residues, 1 model selected > save > /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft_monomer.pdb > selectedOnly true relModel #1 > open > /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_7ZA1_monomer.pdb Chain information for modeller_UNC5D_7ZA1_monomer.pdb #2 --- Chain | Description A | No description available > hide #1 models > show #1 models > select subtract #1 Nothing selected > hide #1 models > show #1 models > ui tool show Matchmaker > matchmaker #2 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 modeller_UNC5D_5fft.pdb, chain E (#1) with modeller_UNC5D_7ZA1_monomer.pdb, chain A (#2), sequence alignment score = 1031.1 RMSD between 197 pruned atom pairs is 1.081 angstroms; (across all 210 pairs: 1.890) > hide #1 models > show #1 models > hide #1 models > hide #2 models > show #2 models > show #1 models > select add #1 3287 atoms, 3329 bonds, 210 residues, 1 model selected > select subtract #1 Nothing selected > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > 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. No residues selected > select add #2 3287 atoms, 3329 bonds, 210 residues, 1 model selected > swapaa interactive sel ALA rotLib Dunbrack No rotamers for ALA in Dunbrack rotamer library > ui tool show Rotamers > swapaa interactive sel ALA rotLib Dunbrack No rotamers for ALA in Dunbrack rotamer library > ui tool show Rotamers > swapaa interactive sel ARG rotLib Dunbrack modeller_UNC5D_7ZA1_monomer.pdb #2/A PRO 1: phi none, psi 9.5 trans Changed 648 bond radii > clashes #!2 & ~#!2/A:1 & ~solvent radius 0.075 reveal true restrict #2.1 & > ~@c,ca,n 83 clashes > hide sel atoms > show sel cartoons > clashes #!2 & ~#!2/A:1 & ~solvent radius 0.075 reveal true restrict #2.1 & > ~@c,ca,n 83 clashes > hide sel atoms > close session > open > /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft_monomer.pdb Chain information for modeller_UNC5D_5fft_monomer.pdb #1 --- Chain | Description E | No description available > open > /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_7ZA1_monomer.pdb Chain information for modeller_UNC5D_7ZA1_monomer.pdb #2 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #2 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 modeller_UNC5D_5fft_monomer.pdb, chain E (#1) with modeller_UNC5D_7ZA1_monomer.pdb, chain A (#2), sequence alignment score = 1031.1 RMSD between 197 pruned atom pairs is 1.081 angstroms; (across all 210 pairs: 1.890) > matchmaker #2 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 modeller_UNC5D_5fft_monomer.pdb, chain E (#1) with modeller_UNC5D_7ZA1_monomer.pdb, chain A (#2), sequence alignment score = 1031.1 RMSD between 197 pruned atom pairs is 1.081 angstroms; (across all 210 pairs: 1.890) > hide #1 models > close #1 > close > open > /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/modeller_UNC5D_5fft_monomer.pdb Chain information for modeller_UNC5D_5fft_monomer.pdb #1 --- Chain | Description E | No description available > ui tool show ""Show Sequence Viewer"" > sequence chain /E Alignment identifier is 1/E > select /E:211 16 atoms, 16 bonds, 1 residue, 1 model selected > select /E 3287 atoms, 3329 bonds, 210 residues, 1 model selected > save /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D/5fft_monomer > format fasta alignment 1/E > hide sel atoms > close session > open 5fft Summary of feedback from opening 5fft fetched from pdb --- notes | Fetching compressed mmCIF 5fft from http://files.rcsb.org/download/5fft.cif Fetching CCD SME from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/SME/SME.cif 5fft title: Crystal Structure of Surfactant Protein-A Y221A Mutant [more info...] Chain information for 5fft #1 --- Chain | Description | UniProt A | Pulmonary surfactant-associated protein A | SFTPA_RAT 81-228 Non-standard residues in 5fft #1 --- CA — calcium ion 5fft mmCIF Assemblies --- 1| author_and_software_defined_assembly 21 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > close session > open 5FTT 5ftt title: Octameric complex of Latrophilin 3 (Lec, Olf) , Unc5D (Ig, Ig2, TSP1) and FLRT2 (LRR) [more info...] Chain information for 5ftt #1 --- Chain | Description | UniProt A E | NETRIN RECEPTOR UNC5D | UNC5D_RAT 32-307 B F | LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN FLRT2 | FLRT2_MOUSE 35-362 C D G H | ADHESION G PROTEIN-COUPLED RECEPTOR L3 | AGRL3_MOUSE 92-463 Non-standard residues in 5ftt #1 --- CA — calcium ion NA — sodium ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > show cartoons > hide atoms > select /F:36-367 2641 atoms, 2698 bonds, 332 residues, 1 model selected > Select #1 Unknown command: Select #1 > Select all Unknown command: Select all > select clear > interfaces ~solvent 14 buried areas: A E 1488, C B 841, G F 803, G H 712, C D 673, B A 626, C A 623, F E 619, G E 618, B D 580, F H 544, B E 485, F A 480, G C 328 > select /A:46-307 2060 atoms, 2115 bonds, 262 residues, 1 model selected > select clear > select /E:45-303 2041 atoms, 2096 bonds, 259 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /A /E Alignment identifier is 1 > select clear > select /A,E:53 20 atoms, 20 bonds, 2 residues, 1 model selected > select /A,E:53-65 226 atoms, 232 bonds, 26 residues, 1 model selected > select /A:304-307/E:45 33 atoms, 33 bonds, 5 residues, 1 model selected > select /E:45 7 atoms, 7 bonds, 1 residue, 1 model selected > select /A:46-52/E:45-52 95 atoms, 98 bonds, 15 residues, 1 model selected > select clear > sequence update /A > close session > open 5FTT 5ftt title: Octameric complex of Latrophilin 3 (Lec, Olf) , Unc5D (Ig, Ig2, TSP1) and FLRT2 (LRR) [more info...] Chain information for 5ftt #1 --- Chain | Description | UniProt A E | NETRIN RECEPTOR UNC5D | UNC5D_RAT 32-307 B F | LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN FLRT2 | FLRT2_MOUSE 35-362 C D G H | ADHESION G PROTEIN-COUPLED RECEPTOR L3 | AGRL3_MOUSE 92-463 Non-standard residues in 5ftt #1 --- CA — calcium ion NA — sodium ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > hide atoms > show atoms > show cartoons > hide atoms > select /B:36-361 2587 atoms, 2642 bonds, 326 residues, 1 model selected > select /F:36-367 2641 atoms, 2698 bonds, 332 residues, 1 model selected > select /C:100-464 2943 atoms, 3026 bonds, 365 residues, 1 model selected Cell requested for row 0 is out of bounds for table with 0 rows! Resizing table model. > select /C:100-464 2943 atoms, 3026 bonds, 365 residues, 1 model selected > delete atoms sel > delete bonds sel > select /D:202-464 2131 atoms, 2191 bonds, 263 residues, 1 model selected > Delete Unknown command: Delete > delete atoms sel > delete bonds sel > select /G:97-464 2968 atoms, 3051 bonds, 368 residues, 1 model selected > delete atoms sel > delete bonds sel > select /H:202-462 2119 atoms, 2179 bonds, 261 residues, 1 model selected > delete atoms sel > delete bonds sel > interfaces ~solvent 5 buried areas: A E 1488, B A 626, F E 619, B E 485, F A 480 > color red > undo > color sel red > color sel hot pink > show sel atoms > hide sel atoms > show sel atoms > show sel cartoons > hide sel atoms > undo > redo > select add #1 9449 atoms, 9669 bonds, 1195 residues, 1 model selected > select subtract #1 Nothing selected > view > ui tool show ""Side View"" > style sphere Changed 9449 atom styles > style stick Changed 9449 atom styles > show surfaces Cell requested for row 0 is out of bounds for table with 2 rows! Resizing table model. > show cartoons > hide surfaces > hide atoms > color (#!1 & sel) red > color (#!1 & sel) hot pink > select clear > view > select clear > color (#!1 & sel) hot pink > color (#!1 & sel) red > color (#!1 & sel) hot pink > ui tool show ""Selection Inspector"" > save /Users/nirakar.basnet/Desktop/image1.png supersample 3 > show sel atoms > show sel cartoons > hide sel surfaces > hide sel atoms > show sel atoms > select clear > show cartoons > hide cartoons > show surfaces > color #1.2 #e0f4c1ff > color #1.2 black > color #1.2 #cadcaeff > color #1.3 #d3ffe4ff > color #1.5 black > color #1.5 #d8ffe4ff > color #1.5 #d8ffe400 > color #1.5 #d8ffe43e > color #1.5 #d8ffe400 > color #1.5 #d8ffe491 > color #1.5 #d8ffe4f7 > hide surfaces > show cartoons > style stick Changed 9449 atom styles > hide atoms > ui windowfill toggle > show surfaces > hide surfaces > save /Users/nirakar.basnet/Desktop/image2.png supersample 3 > interfaces #1/A #1/F #1/E #1/F 3 buried areas: A E 1488, F E 619, F A 480 > select /B/F 5256 atoms, 5370 bonds, 660 residues, 1 model selected > select /A/E 4157 atoms, 4271 bonds, 525 residues, 1 model selected Drag select of 1179 residues > save > /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D_2/UNC5D_5FTT_FLRT_UNC_tetramer.pdb > selectedOnly true relModel #1 > select clear > nucleotides atoms > style nucleic stick Changed 0 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > style stick Changed 9449 atom styles > style stick Changed 9449 atom styles > style sphere Changed 9449 atom styles > hide cartoons > show cartoons > show surfaces > save /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D_2/unc_prep.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 M3 Pro 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 Pro Model Identifier: Mac15,7 Model Number: Z1AK0014ELL/A Chip: Apple M3 Pro Total Number of Cores: 12 (6 performance and 6 efficiency) Memory: 36 GB System Firmware Version: 11881.101.1 OS Loader Version: 11881.101.1 Software: System Software Overview: System Version: macOS 15.4 (24E248) Kernel Version: Darwin 24.4.0 Time since boot: 1 day, 23 hours, 58 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 18 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL P2417H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported 27B2: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 75.00Hz 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