id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9442 Crash deleting tool chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.0-arm64-arm-64bit ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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""b7142778-f6ba-31ca-820c-34b24d90f149"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 5712642048, ""size"" : 144654336, ""uuid"" : ""21c8f378-4426-330a-89d1-26ab67c6fa56"", ""path"" : ""\/Volumes\/VOLUME\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore"", ""name"" : ""QtWebEngineCore"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 4484120576, ""size"" : 20709376, ""uuid"" : ""6b8373ed-7142-34ea-9b4b-9f502e8a6f33"", ""path"" : ""\/Volumes\/VOLUME\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib"", ""name"" : ""libopenblas64_.0.dylib"" }, { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" } ], ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=1.6G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.6G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 768K 6 \nActivity Tracing 256K 1 \nCG backing stores 1344K 4 \nCG image 944K 45 \nColorSync 640K 29 \nCoreAnimation 800K 38 \nCoreGraphics 48K 3 \nCoreServices 432K 3 \nCoreUI image data 4032K 37 \nDispatch continuations 96.0M 1 \nFoundation 208K 3 \nKernel Alloc Once 32K 1 \nMALLOC 756.9M 402 \nMALLOC guard page 192K 11 \nMALLOC_MEDIUM (reserved) 120.0M 1 reserved VM address space (unallocated)\nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 608K 38 \nStack 162.9M 39 \nStack Guard 56.0M 1 \nVM_ALLOCATE 273.3M 369 \nVM_ALLOCATE (reserved) 256.0M 1 reserved VM address space (unallocated)\n__AUTH 1903K 358 \n__AUTH_CONST 24.6M 587 \n__CTF 756 1 \n__DATA 20.0M 719 \n__DATA_CONST 37.1M 727 \n__DATA_DIRTY 1983K 229 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 790.8M 140 \n__OBJC_CONST 4707K 323 \n__OBJC_RO 65.1M 1 \n__OBJC_RW 1981K 1 \n__TEXT 803.2M 749 \ndyld private memory 416K 3 \nmapped file 226.7M 58 \nshared memory 3248K 28 \n=========== ======= ======= \nTOTAL 3.6G 4965 \nTOTAL, minus reserved VM space 3.3G 4965 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""62b4513af75dc926494899c6"", ""factorPackIds"" : { ""COREOS_ICD"" : ""62fbe3cfa9a700130f60b3ea"" }, ""deploymentId"" : 240000019 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000298 } ], ""experiments"" : [ { ""treatmentId"" : ""c28e4ee6-1b08-4f90-8e05-2809e78310a3"", ""experimentId"" : ""6317d2003d24842ff850182a"", ""deploymentId"" : 400000013 } ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__UBP41_HUMAN__998aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb"" Chain information for MYB_HUMAN__UBP41_HUMAN__998aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb #1 --- Chain | Description A | No description available B | No description available > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file ""/Users/jrutter/Dropbox (MIT)/Ebert > Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__UBP41_HUMAN__998aa_scores_rank_001_alphafold2_multimer_v3_model_3_seed_000 > 2.json"" > color #1/A:620-640 lime > color #1/B:27-356 magenta > open ""/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__RN216_HUMAN__1506aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb"" Chain information for MYB_HUMAN__RN216_HUMAN__1506aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb #2 --- Chain | Description A | No description available B | No description available > hide #1 models > color #2 bypolymer > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file ""/Users/jrutter/Dropbox (MIT)/Ebert > Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__RN216_HUMAN__1506aa_scores_rank_001_alphafold2_multimer_v3_model_5_seed_000.json"" Number of residues in structure ""MYB_HUMAN__UBP41_HUMAN__998aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb #1"" is 998 which does not match PAE matrix size 1506. This can happen if chains were deleted from the AlphaFold model or if the PAE data was applied to a structure that was not the one predicted by AlphaFold. Use the full-length AlphaFold model to show predicted aligned error. > ui tool show ""AlphaFold Error Plot"" > alphafold pae #2 file ""/Users/jrutter/Dropbox (MIT)/Ebert > Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__RN216_HUMAN__1506aa_scores_rank_001_alphafold2_multimer_v3_model_5_seed_000.json"" > color #2/A:20-287 lime > color #2/B:306-848 magenta > alphafold pae #2 colorDomains true > color bfactor #2 palette alphafold 12068 atoms, 1506 residues, atom bfactor range 13.1 to 97.1 > color #2 bychain > alphafold contacts #2/A toResidues #2/B > color bfactor #2 palette alphafold 12068 atoms, 1506 residues, atom bfactor range 13.1 to 97.1 > color #!2 bypolymer > open ""/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__FBX7_HUMAN__1162aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb"" Chain information for MYB_HUMAN__FBX7_HUMAN__1162aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #3 --- Chain | Description A | No description available B | No description available > close #2 > color #3 bychain > alphafold contacts #2/A toResidues #2/B No residues specified for alphafold contacts > ui tool show ""AlphaFold Error Plot"" > alphafold pae #3 file ""/Users/jrutter/Dropbox (MIT)/Ebert > Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__FBX7_HUMAN__1162aa_scores_rank_001_alphafold2_multimer_v3_model_2_seed_000.json"" > alphafold contacts #2/A toResidues #2/B No residues specified for alphafold contacts > alphafold contacts #2/A toResidues #2/B No residues specified for alphafold contacts > color #3/A:159-159 lime > color #3/A:325-325 magenta > color #3/A:621-640/B:1-113 magenta > alphafold pae #3 colorDomains true > color bfactor #3 palette alphafold 9209 atoms, 1162 residues, atom bfactor range 12.5 to 97.9 > alphafold contacts #2/A toResidues #2/B No residues specified for alphafold contacts > color bfactor #3 palette alphafold 9209 atoms, 1162 residues, atom bfactor range 12.5 to 97.9 > color #3/A:23-215 lime > color #3/B:17-76 magenta > alphafold contacts #2/A toResidues #2/B No residues specified for alphafold contacts > alphafold contacts #2/A toResidues #2/B No residues specified for alphafold contacts > contacts#2/A to #2/B Unknown command: alphafold contacts#2/A to #2/B > alphafold contacts #2/A toResidues #2/B distance 4 No residues specified for alphafold contacts > select add #3 9209 atoms, 9443 bonds, 1162 residues, 1 model selected > alphafold contacts #2/A toResidues #2/B distance 4 No residues specified for alphafold contacts > color bfactor #3 palette alphafold 9209 atoms, 1162 residues, atom bfactor range 12.5 to 97.9 > alphafold contacts #2/A toResidues #2/B distance 4 No residues specified for alphafold contacts > undo Undo failed, probably because structures have been modified. > undo Undo failed, probably because structures have been modified. > undo Undo failed, probably because structures have been modified. > open ""/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__NOSIP_HUMAN__941aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb"" Chain information for MYB_HUMAN__NOSIP_HUMAN__941aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #2 --- Chain | Description A | No description available B | No description available > close #3 > color #2 bypolymer > color #2 bychain > ui tool show ""AlphaFold Error Plot"" Must choose structure to associate with predicted aligned error > ui tool show ""AlphaFold Error Plot"" > alphafold pae #2 file ""/Users/jrutter/Dropbox (MIT)/Ebert > Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__NOSIP_HUMAN__941aa_scores_rank_001_alphafold2_multimer_v3_model_1_seed_000.json"" > color #2/A:192-192 lime > color #2/A:65-65 magenta > alphafold pae #2 colorDomains true > color #2 bypolymer > color #2 bychain > color #2 bypolymer > show #2 surfaces > alphafold contacts #2/A toResidues #2/B distance 4 > select coil 10503 atoms, 10711 bonds, 4 pseudobonds, 1357 residues, 3 models selected > hide sel & #!2 surfaces > select all 15398 atoms, 15761 bonds, 66 pseudobonds, 1939 residues, 3 models selected > transparency (#!2 & sel) 60 > hide #2.3 models > ui windowfill toggle > show sel & #!2 atoms > mlp sel & #!2 Map values for surface ""MYB_HUMAN__NOSIP_HUMAN__941aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_A SES surface"": minimum -30.39, mean -5.152, maximum 25.31 Map values for surface ""MYB_HUMAN__NOSIP_HUMAN__941aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_B SES surface"": minimum -26.91, mean -4.538, maximum 22.45 To also show corresponding color key, enter the above mlp command and add key true > select coil 10503 atoms, 10711 bonds, 4 pseudobonds, 1357 residues, 3 models selected > hide sel & #!2 atoms > hide sel & #!2 surfaces > ui windowfill toggle > open ""/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__NUSAP_HUMAN__1081aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb"" Chain information for MYB_HUMAN__NUSAP_HUMAN__1081aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #3 --- Chain | Description A | No description available B | No description available > select add #2 12789 atoms, 13059 bonds, 66 pseudobonds, 1630 residues, 5 models selected > hide #!2 models > select subtract #2 5378 atoms, 5478 bonds, 689 residues, 3 models selected > hide #2.1 models > hide #2.2 models > color #3 bychain > open ""/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__KLH41_HUMAN__1246aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb"" Chain information for MYB_HUMAN__KLH41_HUMAN__1246aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb #4 --- Chain | Description A | No description available B | No description available > hide #3 models > color #4 bychain > color #4 bypolymer > open ""/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__FBXL8_HUMAN__1014aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb"" Chain information for MYB_HUMAN__FBXL8_HUMAN__1014aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #5 --- Chain | Description A | No description available B | No description available > hide #4 models > color #5 bypolymer > open ""/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__UBE3A_HUMAN__1515aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb"" Chain information for MYB_HUMAN__UBE3A_HUMAN__1515aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb #6 --- Chain | Description A | No description available B | No description available > hide #6 models > show #6 models > hide #5 models > color #6 bypolymer > color #6 bychain > close #6 > open ""/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__UBE3C_HUMAN__1723aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb"" Chain information for MYB_HUMAN__UBE3C_HUMAN__1723aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #6 --- Chain | Description A | No description available B | No description available > color #6 bychain > open ""/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__RFPLB_HUMAN__903aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb"" Chain information for MYB_HUMAN__RFPLB_HUMAN__903aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb #7 --- Chain | Description A | No description available B | No description available > hide #6 models > color #7 bypolymer > color #7 bychain > open ""/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__KLH41_HUMAN__1246aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb"" Chain information for MYB_HUMAN__KLH41_HUMAN__1246aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb #8 --- Chain | Description A | No description available B | No description available > hide #7 models > color #8 bypolymer > open ""/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__MEX3C_HUMAN__1299aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"" Chain information for MYB_HUMAN__MEX3C_HUMAN__1299aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #9 --- Chain | Description A | No description available B | No description available > hide #8 models > color #9 bychain > color #9 bypolymer > open ""/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__EP300_HUMAN__3054aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb"" Chain information for MYB_HUMAN__EP300_HUMAN__3054aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #10 --- Chain | Description A | No description available B | No description available > hide #9 models > color #10 bypolymer > color #10 bychain > view sel > hide #10 models > open ""/Users/jrutter/Dropbox (MIT)/MYB_KIFC1_cleanup.cxs"" ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open ""/Users/jrutter/Dropbox (MIT)/MYB_KIFC1_cleanup.cxs"" Log from Sat Jul 22 22:07:52 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show AlphaFold Populating font family aliases took 137 ms. Replace uses of missing font family ""Lato"" with one that exists to avoid this cost. > alphafold predict > MEDEEGPEYGKPDFVLLDQVTMEDFMRNLQLRFEKGRIYTYIGEVLVSVNPYQELPLYGPEAIARYQGRELYERPPHLYAVANAAYKAMKHRSRDTCIVISGESGAGKTEASKHIMQYIAAVTNPSQRAEVERVKDVLLKSTCVLEAFGNARTNRNHNSSRFGKYMDINFDFKGDPIGGHIHSYLLEKSRVLKQHVGERNFHAFYQLLRGSEDKQLHELHLERNPAVYNFTHQGAGLNMTVHSALDSDEQSHQAVTEAMRVIGFSPEEVESVHRILAAILHLGNIEFVETEEGGLQKEGLAVAEEALVDHVAELTATPRDLVLRSLLARTVASGGRELIEKGHTAAEASYARDACAKAVYQRLFEWVVNRINSVMEPRGRDPRRDGKDTVIGVLDIYGFEVFPVNSFEQFCINYCNEKLQQLFIQLILKQEQEEYEREGITWQSVEYFNNATIVDLVERPHRGILAVLDEACSSAGTITDRIFLQTLDMHHRHHLHYTSRQLCPTDKTMEFGRDFRIKHYAGDVTYSVEGFIDKNRDFLFQDFKRLLYNSTDPTLRAMWPDGQQDITEVTKRPLTAGTLFKNSMVALVENLASKEPFYVRCIKPNEDKVAGKLDENHCRHQVAYLGLLENVRVRRAGFASRQPYSRFLLRYKMTCEYTWPNHLLGSDKAAVSALLEQHGLQGDVAFGHSKLFIRSPRTLVTLEQSRARLIPIIVLLLQKAWRGTLARWRCRRLRAIYTIMRWFRRHKVRAHLAELQRRFQAARQPPLYGRDLVWPLPPAVLQPFQDTCHALFCRWRARQLVKNIPPSDMPQIKAKVAAMGALQGLRQDWGCRRAWARDYLSSATDNPTASSLFAQRLKTLQDKDGFGAVLFSSHVRKVNRFHKIRNRALLLTDQHLYKLDPDRQYRVMRAVPLEAVTGLSVTSGGDQLVVLHARGQDDLVVCLHRSRPPLDNRVGELVGVLAAHCQGEGRTLEVRVSDCIPLSHRGVRRLISVEPRPEQPEPDFRCARGSFTLLWPSR,PAAAAIQRHYNDEDPEKEKRIKELELLLMSTENELKGQQVLPTQNHTCSYPGW Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions. Running AlphaFold prediction > open ""/Users/jrutter/Dropbox (MIT)/Ebert Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"" Chain information for MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1 --- Chain | Description A | No description available B | No description available Drag select of 184 residues > delete atoms sel > delete bonds sel Drag select of 86 residues > delete atoms sel > delete bonds sel Drag select of 60 residues > delete atoms sel > delete bonds sel Drag select of 2 residues > delete atoms sel > delete bonds sel > select clear > ui tool show ""Side View"" Drag select of 58 residues > delete atoms sel > delete bonds sel Drag select of 82 residues, 2 pseudobonds > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) Drag select of 18 residues, 1 pseudobonds > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) Drag select of 10 residues, 1 pseudobonds > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) Drag select of 7 residues > delete atoms sel > delete bonds sel > color bypolymer > set bgColor white > lighting flat > view Drag select of 1 pseudobonds No visible atoms or bonds selected > hide cartoons > show cartoons > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file ""/Users/jrutter/Dropbox (MIT)/Ebert > Lab/Ebert_computational/Alphafold > screen/remote_job_0000742_longley/MYB_HUMAN__KIFC1_HUMAN__1313aa_scores_rank_001_alphafold2_multimer_v3_model_4_seed_000.json"" > alphafold pae #1 colorDomains true > color bfactor #1 palette alphafold 6401 atoms, 806 residues, atom bfactor range 14.9 to 97.4 Drag select of 6 residues, 1 pseudobonds Drag select of 37 residues > delete atoms sel > delete bonds sel Drag select of 10 residues, 1 pseudobonds > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) Drag select of 7 residues > delete atoms sel > delete bonds sel > select clear Drag select of 12 residues, 1 pseudobonds > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) Drag select of 2 residues > delete atoms sel > delete bonds sel > hide cartoons > show cartoons > save ""/Users/jrutter/Dropbox (MIT)/MYB_KIFC1_cleanup.cxs"" > show surfaces > rainbow > color bypolymer Drag select of MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A SES surface, 2942 of 235002 triangles Drag select of MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A SES surface, 2958 of 235002 triangles [Repeated 1 time(s)] > select clear Drag select of MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A SES surface, 2958 of 235002 triangles > hide surfaces > show surfaces > transparency #1.2 70 Drag select of MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B SES surface, 57189 of 580510 triangles, 67 residues > transparency (#!1 & sel) 70 Drag select of MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A SES surface, MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B SES surface, 735 residues > transparency (#!1 & sel) 70 > ui tool show ""AlphaFold Error Plot"" > color bfactor #1 palette alphafold 5865 atoms, 738 residues, 2 surfaces, atom bfactor range 14.9 to 97.4 > transparency (#!1 & sel) 60 Drag select of MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A SES surface, 6498 of 235002 triangles, MYB_HUMAN__KIFC1_HUMAN__1313aa_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B SES surface, 9033 of 580510 triangles, 17 residues > color #1/B:163-198 lime > color #1/B:240-673 magenta > color #1/A:56-86 lime > color #1/B:290-673 magenta > color bfactor #1 palette alphafold 5865 atoms, 738 residues, 2 surfaces, atom bfactor range 14.9 to 97.4 > color #1/A:54-78 lime > color #1/B:306-673 magenta > alphafold contacts #1/A toResidues #1/B > transparency (#!1 & sel) 60 > color bfactor #1 palette alphafold 5865 atoms, 738 residues, 2 surfaces, atom bfactor range 14.9 to 97.4 > select all 5865 atoms, 5959 bonds, 28 pseudobonds, 738 residues, 3 models selected > color bfactor #1 palette alphafold 5865 atoms, 738 residues, 2 surfaces, atom bfactor range 14.9 to 97.4 > transparency (#!1 & sel) 60 > alphafold contacts #1/A toResidues #1/B distance 4 > alphafold contacts #1/A toResidues #1/B distance 4 color pLDDT Expected a keyword > color bfactor #1 palette alphafold 5865 atoms, 738 residues, 2 surfaces, atom bfactor range 14.9 to 97.4 > transparency (#!1 & sel) 60 > save ""/Users/jrutter/Dropbox (MIT)/MYB_KIFC1_cleanup.cxs"" ——— End of log from Sat Jul 22 22:07:52 2023 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M2 Max OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,5 Model Number: MPHK3LL/A Chip: Apple M2 Max Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 32 GB System Firmware Version: 8419.41.10 OS Loader Version: 8419.41.10 Software: System Software Overview: System Version: macOS 13.0 (22A8380) Kernel Version: Darwin 22.1.0 Time since boot: 13 days, 6 hours, 46 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 30 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: DELL U3415W: Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD) UI Looks like: 3440 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0 }}} " defect closed normal UI can't reproduce all ChimeraX