id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14827 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.4-arm64-arm-64bit ChimeraX Version: 1.6rc202304202331 (2023-04-20 23:31:10 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6246d6a916a70b047e454124"", ""factorPackIds"" : { }, ""deploymentId"" : 240000010 }, { ""rolloutId"" : ""61675b89201f677a9a4cbd65"", ""factorPackIds"" : { ""HEALTH_FEATURE_AVAILABILITY"" : ""65a855f5f087695cfac03d1f"" }, ""deploymentId"" : 240000095 } ], ""experiments"" : [ { ""treatmentId"" : ""a3f9ec09-b145-49f3-8142-da4a1f338456"", ""experimentId"" : ""65f21aa774b6f500a45abd7d"", ""deploymentId"" : 400000002 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6rc202304202331 (2023-04-20) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/jo_air/Dropbox/CBG LAB/Collaborations/Gallego- > Bartolome/Results/results_MINU_reduced/results_MINUred_ARP4_ARP7_RTT102/results(18)/best_model.pdb"" > format pdb Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > color bychain > ui tool show ""Show Sequence Viewer"" > sequence chain /D Alignment identifier is 1/D > select /D:3-12,46-51,123-129 349 atoms, 347 bonds, 23 residues, 1 model selected > select /D:24-30,58-66,81-83 369 atoms, 376 bonds, 19 residues, 1 model selected > select /D:88 12 atoms, 11 bonds, 1 residue, 1 model selected > select /D:1-88 1458 atoms, 1476 bonds, 88 residues, 1 model selected > select clear > select /D:110 7 atoms, 6 bonds, 1 residue, 1 model selected > select /D:110-111 17 atoms, 16 bonds, 2 residues, 1 model selected > select /D:3-12,46-51,123-129 349 atoms, 347 bonds, 23 residues, 1 model selected > select /D:51-52 28 atoms, 27 bonds, 2 residues, 1 model selected > select /D:1-52 828 atoms, 839 bonds, 52 residues, 1 model selected > select /D:110 7 atoms, 6 bonds, 1 residue, 1 model selected > select /D:110 7 atoms, 6 bonds, 1 residue, 1 model selected > select /D:21 11 atoms, 10 bonds, 1 residue, 1 model selected > select /D:21-71 868 atoms, 881 bonds, 51 residues, 1 model selected > select /D:109 14 atoms, 13 bonds, 1 residue, 1 model selected > select /D:109-110 21 atoms, 20 bonds, 2 residues, 1 model selected > select /D:20 14 atoms, 13 bonds, 1 residue, 1 model selected > select /D:20-76 971 atoms, 984 bonds, 57 residues, 1 model selected > select coil 6744 atoms, 6737 bonds, 461 residues, 1 model selected > close session > ui tool show AlphaFold Populating font family aliases took 146 ms. Replace uses of missing font family ""Calibri"" with one that exists to avoid this cost. QCssParser::parseHexColor: Unknown color name '#0C00' > alphafold predict > MEALVVDAGSKFLKAGAAIPDQSPAMIIPSQMKRMVDDGSSSADNPTTVFEDVTLDPIERGLIRDWDAMEDLLRYVVYTGLGWEEGNEGNILFTDPLCTPKAIREQLVQLMFETFNVSGFYASEQAVLSLYAVGRISGCTVDIGHGKIDIAPVLEGAVQHIASKRFELGGTELTKLFAQELGKTNPSMNLSMSDVEKLKEQYANCAEDEIAYKKTQNCEIEQHTLPDGQVISIGRERYSVGEALFQPSILGLEEHGIVEQLVRIISTVSSENHRQLLENTVLCGGTTSMTGFESRFQKEANLCSSAIRPTLVKPPEYMPENLGMYSAWVGGAILAKVVFPQNQHVTKADYDETGPSVVHRKCF,MDPQTLITKANKVSYYGNPTSKESWRYDWYQPSKVSSNVQQPQQQLGDMENNLEKYPFRYKTWLRNQEDEKNLQRESCEDILDLKEFDRRILKKSLMTSHTKGDTSKATGAPSANQGDEALSVDDIRGAVGNSEAIPGLSAGVNNDNTKESKDVKMN AlphaFold Service Broken ## AlphaFold Prediction Requires Newer ChimeraX Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or later. The ChimeraX AlphaFold prediction service was broken by an update on Google Colab on March 14, 2024. > ui tool show Updates > open ""/Users/jo_air/Dropbox/CBG LAB/Collaborations/Orzaez/RMSD.cxs"" format > session opened ChimeraX session > close session > open ""/Users/jo_air/Dropbox/CBG LAB/Collaborations/Gallego- > Bartolome/Results/results_MINU_reduced/results_MINUred_ARP4_ARP7_RTT102quimeraBDH1/results(19)/best_model.pdb"" > format pdb Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > color bychain > open ""/Users/jo_air/Dropbox/CBG LAB/Collaborations/Gallego- > Bartolome/Results/results_MINU_reduced/results_MINUred_ARP4_ARP7_BDH1/best_model.pdb"" Chain information for best_model.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > close session > open ""/Users/jo_air/Dropbox/CBG LAB/Collaborations/Gallego- > Bartolome/Results/results_MINU_reduced/results_MINUred_ARP4_ARP7_BDH1/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > open ""/Users/jo_air/Dropbox/CBG LAB/Collaborations/Gallego- > Bartolome/Results/Matchmaker_BDH1_ARP7_ARP4_to_ARP7_ARP9_Rtt102_2.cxs"" ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6rc202304202331 (2023-04-20) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/jo_air/Dropbox/CBG LAB/Collaborations/Gallego- > Bartolome/Results/Matchmaker_BDH1_ARP7_ARP4_to_ARP7_ARP9_Rtt102_2.cxs"" Log from Thu Feb 1 23:40:16 2024UCSF ChimeraX version: 1.6rc202304202331 (2023-04-20) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/jo_air/Desktop/BDH1_ARP7_ARP4.cxs format session Log from Thu Feb 1 12:01:04 2024UCSF ChimeraX version: 1.6rc202304202331 (2023-04-20) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/jo_air/Downloads/results(3)/best_model.pdb Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > select /A 6821 atoms, 6889 bonds, 441 residues, 1 model selected > show sel surfaces > select /B 5560 atoms, 5612 bonds, 363 residues, 1 model selected > show sel surfaces > color (#!1 & sel) light sea green > select /C 3594 atoms, 3618 bonds, 238 residues, 1 model selected > show sel surfaces > color (#!1 & sel) hot pink > select clear > lighting simple > lighting soft > color bychain > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.1: minimum, -13.04, mean -1.66, maximum 15.51 Coulombic values for best_model.pdb_B SES surface #1.2: minimum, -20.82, mean -3.04, maximum 8.17 Coulombic values for best_model.pdb_C SES surface #1.3: minimum, -15.53, mean -1.88, maximum 15.76 To also show corresponding color key, enter the above coulombic command and add key true > color bychain > select /C 3594 atoms, 3618 bonds, 238 residues, 1 model selected > hide sel surfaces > select clear > select /B:118@O 1 atom, 1 residue, 1 model selected > select /C:1 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 453 atoms, 458 bonds, 29 residues, 2 models selected > show sel atoms > color sel byhetero > show (#!1 & sel-residues & sidechain) target ab > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel stick Changed 453 atom styles > select clear > select /C:23 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 453 atoms, 458 bonds, 29 residues, 2 models selected > show sel atoms > hide sel atoms > show sel atoms > select H 7903 atoms, 1042 residues, 1 model selected > hide sel atoms > select clear > select /C:27 22 atoms, 21 bonds, 1 residue, 1 model selected > select up 453 atoms, 458 bonds, 29 residues, 2 models selected > ui tool show H-Bonds > hbonds sel interModel false intraMol false intraRes false select true reveal > true 5 hydrogen bonds found > hbonds sel interModel false intraMol false intraRes false select true reveal > true 5 hydrogen bonds found > show sel atoms > transparency (#!1 & sel) 30 > transparency (#!1 & sel) 70 > color sel byhetero > select clear > select /C:76 22 atoms, 21 bonds, 1 residue, 1 model selected > select up 91 atoms, 94 bonds, 5 residues, 2 models selected > show sel atoms > color sel byhetero > select H 7903 atoms, 1042 residues, 1 model selected > hide (#!1 & sel) target a > select clear > select /C:77 24 atoms, 25 bonds, 1 residue, 1 model selected > select up 91 atoms, 94 bonds, 5 residues, 2 models selected > ui tool show H-Bonds > hbonds sel interModel false intraMol false intraRes false select true reveal > true 1 hydrogen bonds found > hbonds sel interModel false intraMol false intraRes false select true reveal > true 1 hydrogen bonds found > transparency (#!1 & sel) 70 > color sel byhetero > select /C:30 22 atoms, 21 bonds, 1 residue, 1 model selected > select up 101 atoms, 103 bonds, 5 residues, 2 models selected > show sel atoms > color sel byhetero > select H 7903 atoms, 1042 residues, 1 model selected > hide (#!1 & sel) target a > select clear > select /C:31 22 atoms, 21 bonds, 1 residue, 1 model selected > select up 101 atoms, 103 bonds, 5 residues, 2 models selected > ui tool show H-Bonds > hbonds sel interModel false intraMol false intraRes false select true reveal > true 2 hydrogen bonds found > hbonds sel interModel false intraMol false intraRes false select true reveal > true 2 hydrogen bonds found > transparency (#!1 & sel) 70 > color sel byhetero > select clear > select /C:116 21 atoms, 21 bonds, 1 residue, 1 model selected > select up 93 atoms, 95 bonds, 5 residues, 2 models selected > show sel atoms > color sel byhetero > select H 7903 atoms, 1042 residues, 1 model selected > hide (#!1 & sel) target a > select clear > select /C:115 22 atoms, 21 bonds, 1 residue, 1 model selected > select up 93 atoms, 95 bonds, 5 residues, 2 models selected > ui tool show H-Bonds > hbonds sel interModel false intraMol false intraRes false select true reveal > true 5 hydrogen bonds found > hbonds sel interModel false intraMol false intraRes false select true reveal > true 5 hydrogen bonds found > show sel atoms > transparency (#!1 & sel) 80 > color sel byhetero > select clear > view > save /Users/jo_air/Desktop/BDH-ARP7-ARP4.tif width 1500 height 1266 > supersample 3 transparentBackground true > save /Users/jo_air/Desktop/BDH-ARP7-ARP4.tif width 2000 height 1688 > supersample 3 transparentBackground true > save /Users/jo_air/Desktop/BDH-ARP7-ARP4.png width 3000 height 2531 > supersample 3 transparentBackground true > save /Users/jo_air/Desktop/BDH-ARP7-ARP4.png width 4000 height 3375 > supersample 3 transparentBackground true Alignment identifier is 1/A Alignment identifier is 1/B Alignment identifier is 1/C > select /A:119@O 1 atom, 1 residue, 1 model selected > view sel > select clear > view > select /C:30 22 atoms, 21 bonds, 1 residue, 1 model selected > select up 101 atoms, 103 bonds, 5 residues, 2 models selected > ui tool show H-Bonds > hbonds sel interModel false intraMol false intraRes false select true reveal > true 2 hydrogen bonds found > hbonds sel interModel false intraMol false intraRes false select true reveal > true 2 hydrogen bonds found > select /C:78 10 atoms, 9 bonds, 1 residue, 1 model selected > select up 91 atoms, 94 bonds, 5 residues, 2 models selected > ui tool show H-Bonds > hbonds sel interModel false intraMol false intraRes false select true reveal > true 1 hydrogen bonds found > hbonds sel interModel false intraMol false intraRes false select true reveal > true 1 hydrogen bonds found > color sel byhetero > select /C:32 24 atoms, 25 bonds, 1 residue, 1 model selected > select up 101 atoms, 103 bonds, 5 residues, 2 models selected > ui tool show H-Bonds > hbonds sel interModel false intraRes false select true reveal true 8 hydrogen bonds found > hbonds sel interModel false intraRes false select true reveal true 8 hydrogen bonds found > select clear > save /Users/jo_air/Desktop/BDH1_ARP7_ARP4.cxs > coulombic Coulombic values for best_model.pdb_A SES surface #1.1: minimum, -13.04, mean -1.66, maximum 15.51 Coulombic values for best_model.pdb_B SES surface #1.2: minimum, -20.82, mean -3.04, maximum 8.17 Coulombic values for best_model.pdb_C SES surface #1.3: minimum, -15.53, mean -1.88, maximum 15.76 To also show corresponding color key, enter the above coulombic command and add key true > ui tool show Contacts > hide surfaces > show surfaces > color byhetero > mlp Map values for surface ""best_model.pdb_A SES surface"": minimum -30.64, mean -5.078, maximum 23.68 Map values for surface ""best_model.pdb_B SES surface"": minimum -29.42, mean -4.612, maximum 24.31 Map values for surface ""best_model.pdb_C SES surface"": minimum -26.88, mean -5.314, maximum 23.39 To also show corresponding color key, enter the above mlp command and add key true > hide surfaces > show surfaces > color bypolymer > color bychain > color bypolymer > color bychain > color bfactor 15975 atoms, 1042 residues, 3 surfaces, atom bfactor range 14.8 to 98.7 > hide surfaces > color bychain > show surfaces > select /C 3594 atoms, 3618 bonds, 6 pseudobonds, 238 residues, 2 models selected > hide sel surfaces > color sel byhetero > select clear > select /C:10 24 atoms, 23 bonds, 1 residue, 1 model selected > select up 453 atoms, 458 bonds, 29 residues, 2 models selected > ui tool show Contacts > contacts sel intraMol false ignoreHiddenModels true select true reveal true 138 contacts > contacts sel intraMol false ignoreHiddenModels true select true reveal true 138 contacts > transparency (#!1 & sel) 80 > color sel byhetero > select clear > select /C:17 14 atoms, 14 bonds, 1 residue, 1 model selected > select up 453 atoms, 458 bonds, 29 residues, 2 models selected > select H 7903 atoms, 11 pseudobonds, 1042 residues, 2 models selected > hide (#!1 & sel) target a > select clear > select solvent Nothing selected > select /C:30 22 atoms, 21 bonds, 1 residue, 1 model selected > select down 22 atoms, 21 bonds, 1 residue, 2 models selected > select up 101 atoms, 103 bonds, 5 residues, 2 models selected > select up 3594 atoms, 3618 bonds, 238 residues, 2 models selected > select down 101 atoms, 103 bonds, 5 residues, 2 models selected > select up 3594 atoms, 3618 bonds, 238 residues, 2 models selected > select down 101 atoms, 103 bonds, 5 residues, 2 models selected > ui tool show Contacts > contacts sel intraMol false ignoreHiddenModels true select true reveal true 58 contacts > contacts sel intraMol false ignoreHiddenModels true select true reveal true 81 contacts > transparency (#!1 & sel) 80 > color sel byhetero > select /A:23@CE1 1 atom, 1 residue, 1 model selected > select clear > save /Users/jo_air/Desktop/BDH1_ARP7_ARP4.cxs ——— End of log from Thu Feb 1 12:01:04 2024 ——— opened ChimeraX session > open /Users/jo_air/Downloads/5tgc.pdb format pdb 5tgc.pdb title: Structure of the hetero-trimer of RTT102-ARP7/9 bound to atp [more info...] Chain information for 5tgc.pdb #2 --- Chain | Description | UniProt A D | actin-related protein 7 | ARP7_YEAST 1-477 B E | actin-like protein ARP9 | ARP9_YEAST 1-467 C F | regulator of TY1 transposition protein 102 | RT102_YEAST 1-157 Non-standard residues in 5tgc.pdb #2 --- ATP — adenosine-5'-triphosphate SO4 — sulfate ion > select #2/B 6327 atoms, 6385 bonds, 4 pseudobonds, 397 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/A 6610 atoms, 6680 bonds, 4 pseudobonds, 408 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/C 1132 atoms, 1147 bonds, 2 pseudobonds, 67 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/D:61@CD 1 atom, 1 residue, 1 model selected > select add #2 14209 atoms, 14360 bonds, 8 pseudobonds, 883 residues, 2 models selected > style sel stick Changed 14209 atom styles > hide sel atoms > show sel cartoons > select clear > save /Users/jo_air/Desktop/homol.cxs > ui tool show Matchmaker > matchmaker #!2 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 best_model.pdb, chain A (#1) with 5tgc.pdb, chain D (#2), sequence alignment score = 524.3 RMSD between 227 pruned atom pairs is 1.146 angstroms; (across all 372 pairs: 13.451) > matchmaker #!2 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 best_model.pdb, chain A (#1) with 5tgc.pdb, chain D (#2), sequence alignment score = 524.3 RMSD between 227 pruned atom pairs is 1.146 angstroms; (across all 372 pairs: 13.451) > select add #1 15975 atoms, 16119 bonds, 89 pseudobonds, 1042 residues, 3 models selected > hide sel surfaces > select clear > save /Users/jo_air/Desktop/Matchmaker_BDH1_ARP7_ARP4_to_ARP7_ARP9_Rtt102.cxs > save > /Users/jo_air/Desktop/Matchmaker_BDH1_ARP7_ARP4_to_ARP7_ARP9_Rtt102_1.png > width 6000 height 3816 supersample 3 transparentBackground true > select #1/C:77 24 atoms, 25 bonds, 1 residue, 1 model selected > select up 91 atoms, 94 bonds, 5 residues, 2 models selected > select up 3594 atoms, 3618 bonds, 238 residues, 2 models selected > select down 91 atoms, 94 bonds, 5 residues, 2 models selected > view sel > select clear > select #1/C:77 24 atoms, 25 bonds, 1 residue, 1 model selected > select up 91 atoms, 94 bonds, 5 residues, 2 models selected > hide sel atoms > select #1/C:32 24 atoms, 25 bonds, 1 residue, 1 model selected > select up 101 atoms, 103 bonds, 5 residues, 2 models selected > hide sel atoms > select clear > save > /Users/jo_air/Desktop/Matchmaker_BDH1_ARP7_ARP4_to_ARP7_ARP9_Rtt102_2.png > width 6000 height 3816 supersample 3 transparentBackground true > select clear > select #1/A 6821 atoms, 6889 bonds, 441 residues, 1 model selected > show sel surfaces > select #1/B 5560 atoms, 5612 bonds, 363 residues, 1 model selected > show sel surfaces > select #1/C 3594 atoms, 3618 bonds, 6 pseudobonds, 238 residues, 2 models selected > select #2/E 6270 atoms, 6334 bonds, 3 pseudobonds, 392 residues, 2 models selected > show sel surfaces > select #2/D 6895 atoms, 6967 bonds, 3 pseudobonds, 429 residues, 2 models selected > show sel surfaces > select clear [Repeated 1 time(s)] > view > select clear [Repeated 1 time(s)] > save > /Users/jo_air/Desktop/Matchmaker_BDH1_ARP7_ARP4_to_ARP7_ARP9_Rtt102_3.png > width 6000 height 3816 supersample 3 transparentBackground true > select #2/F:29 24 atoms, 25 bonds, 1 residue, 1 model selected > select up 126 atoms, 131 bonds, 6 residues, 1 model selected > select up 588 atoms, 598 bonds, 36 residues, 1 model selected > select down 126 atoms, 131 bonds, 6 residues, 1 model selected > view sel > select clear [Repeated 1 time(s)] > transparency 40 > transparency 20 > transparency 0 > save > /Users/jo_air/Desktop/Matchmaker_BDH1_ARP7_ARP4_to_ARP7_ARP9_Rtt102_4.png > width 6000 height 3816 supersample 3 transparentBackground true > save > /Users/jo_air/Desktop/Matchmaker_BDH1_ARP7_ARP4_to_ARP7_ARP9_Rtt102_2.cxs ——— End of log from Thu Feb 1 23:40:16 2024 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac14,2 Model Number: Z161000GJY/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8422.121.1 OS Loader Version: 8422.121.1 Software: System Software Overview: System Version: macOS 13.4 (22F66) Kernel Version: Darwin 22.5.0 Time since boot: 4 days, 1 hour, 54 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9 ChimeraX-AddH: 2.2.4 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 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: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6rc202304202331 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 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: 1.2.1 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: 1.1.4 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 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-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 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: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 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: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.2.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Core duplicate all ChimeraX