id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8727 AlphaFold: Downloaded prediction file not found chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.2.1-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. Fatal Python error: Segmentation fault Thread 0x000000029c02b000 (most recent call first): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000029b01f000 (most recent call first): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000029a013000 (most recent call first): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 416 in select File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py"", line 936 in wait File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 499 in _wait_for_updates File 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minus reserved VM space 4.2G 4887 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000255 }, { ""rolloutId"" : ""63a0a6cfd1cdb67d083006d0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000003 } ], ""experiments"" : [ ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== You can double click a model's Name or ID in the model panel to edit those fields UCSF 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 > alphafold predict > MSTLQRRRVNRADSGDTSSIHSSANNTKGDKIANIAVDGDDDNGTNKKIAYDPEESKLRDNINIPTLTLMEEVLLMGLRDREGYLSFWNDSISYALRGCIIIELALRGKIRILDDSARKRFDLSERLIEVIDSSKTGEVLLDETLQLMKNDEPLSISNWIDLLSGETWNLLKINYQLKQVRERLAKGLVDKGVLRTEMKNFFLFDMATHPIADASCKEAIKRRVLSVLVSRNMELSYNEYFPETTSFKIIRTLALICGSYGANVLENVLTTLEYEKRDKAISRAEEIMAQFSQYPFDLEKETELGVSVNLNKEVKEEIENNPGHDLQLEVIAGVFEVFSRMDMLL,MSTLQRRRVNRADSGDTSSIHSSANNTKGDKIANIAVDGDDDNGTNKKIAYDPEESKLRDNINIPTLTLMEEVLLMGLRDREGYLSFWNDSISYALRGCIIIELALRGKIRILDDSARKRFDLSERLIEVIDSSKTGEVLLDETLQLMKNDEPLSISNWIDLLSGETWNLLKINYQLKQVRERLAKGLVDKGVLRTEMKNFFLFDMATHPIADASCKEAIKRRVLSVLVSRNMELSYNEYFPETTSFKIIRTLALICGSYGANVLENVLTTLEYEKRDKAISRAEEIMAQFSQYPFDLEKETELGVSVNLNKEVKEEIENNPGHDLQLEVIAGVFEVFSRMDMLL,MSTLQRRRVNRADSGDTSSIHSSANNTKGDKIANIAVDGDDDNGTNKKIAYDPEESKLRDNINIPTLTLMEEVLLMGLRDREGYLSFWNDSISYALRGCIIIELALRGKIRILDDSARKRFDLSERLIEVIDSSKTGEVLLDETLQLMKNDEPLSISNWIDLLSGETWNLLKINYQLKQVRERLAKGLVDKGVLRTEMKNFFLFDMATHPIADASCKEAIKRRVLSVLVSRNMELSYNEYFPETTSFKIIRTLALICGSYGANVLENVLTTLEYEKRDKAISRAEEIMAQFSQYPFDLEKETELGVSVNLNKEVKEEIENNPGHDLQLEVIAGVFEVFSRMDMLL,MSTLQRRRVNRADSGDTSSIHSSANNTKGDKIANIAVDGDDDNGTNKKIAYDPEESKLRDNINIPTLTLMEEVLLMGLRDREGYLSFWNDSISYALRGCIIIELALRGKIRILDDSARKRFDLSERLIEVIDSSKTGEVLLDETLQLMKNDEPLSISNWIDLLSGETWNLLKINYQLKQVRERLAKGLVDKGVLRTEMKNFFLFDMATHPIADASCKEAIKRRVLSVLVSRNMELSYNEYFPETTSFKIIRTLALICGSYGANVLENVLTTLEYEKRDKAISRAEEIMAQFSQYPFDLEKETELGVSVNLNKEVKEEIENNPGHDLQLEVIAGVFEVFSRMDMLL Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions. Running AlphaFold prediction AlphaFold prediction finished Results in /Users/fearjuan/Downloads/ChimeraX/AlphaFold/prediction_4 > open > /Users/fearjuan/Downloads/ChimeraX/AlphaFold/prediction_4/best_model.pdb Chain information for best_model.pdb #1 --- Chain | Description B C D E | No description available > alphafold predict > MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK,MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK > directory /Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer Running AlphaFold prediction AlphaFold prediction finished Results in /Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer Downloaded prediction file not found: /Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer/best_model.pdb > alphafold predict > MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK,MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK > directory /Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer Running AlphaFold prediction AlphaFold prediction finished Results in /Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer Downloaded prediction file not found: /Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer/best_model.pdb > alphafold predict > MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK,MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK,MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK,MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK > directory > /Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpintetramer Running AlphaFold prediction AlphaFold prediction finished Results in /Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpintetramer Downloaded prediction file not found: /Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpintetramer/best_model.pdb > alphafold predict > MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK,MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK,MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK,MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK > directory > /Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpintetramer Running AlphaFold prediction > open > ""/Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer/results > (1)/af564_unrelaxed_rank_1_model_2.pdb"" Chain information for af564_unrelaxed_rank_1_model_2.pdb #2 --- Chain | Description B C | No description available > open > ""/Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer/results > (1)/af564_unrelaxed_rank_2_model_5.pdb"" Chain information for af564_unrelaxed_rank_2_model_5.pdb #3 --- Chain | Description B C | No description available > open > ""/Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer/results > (1)/af564_unrelaxed_rank_3_model_3.pdb"" Chain information for af564_unrelaxed_rank_3_model_3.pdb #4 --- Chain | Description B C | No description available > open > ""/Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer/results > (1)/af564_unrelaxed_rank_4_model_4.pdb"" Chain information for af564_unrelaxed_rank_4_model_4.pdb #5 --- Chain | Description B C | No description available > open > ""/Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer/results > (1)/af564_unrelaxed_rank_5_model_1.pdb"" Chain information for af564_unrelaxed_rank_5_model_1.pdb #6 --- Chain | Description B C | No description available > open > ""/Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer/results > (1)/best_model.pdb"" Chain information for best_model.pdb #7 --- Chain | Description B C | No description available > hide #1 models > ui mousemode right zoom > ui mousemode right rotate > ui mousemode right translate > hide #2 models > hide #3 models > hide #4 models > hide #5 models > hide #6 models > coulombic #7 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_B SES surface #7.1: minimum, -15.27, mean -1.39, maximum 14.62 Coulombic values for best_model.pdb_C SES surface #7.2: minimum, -15.65, mean -1.42, maximum 17.07 To also show corresponding color key, enter the above coulombic command and add key true > color #!7 byhetero > color #!7 bychain > coulombic #!7 Coulombic values for best_model.pdb_B SES surface #7.1: minimum, -15.27, mean -1.39, maximum 14.62 Coulombic values for best_model.pdb_C SES surface #7.2: minimum, -15.65, mean -1.42, maximum 17.07 To also show corresponding color key, enter the above coulombic command and add key true > mlp #!7 Map values for surface ""best_model.pdb_B SES surface"": minimum -27.01, mean -6.046, maximum 23.08 Map values for surface ""best_model.pdb_C SES surface"": minimum -27.29, mean -6.069, maximum 24.22 To also show corresponding color key, enter the above mlp command and add key true > coulombic #!7 Coulombic values for best_model.pdb_B SES surface #7.1: minimum, -15.27, mean -1.39, maximum 14.62 Coulombic values for best_model.pdb_C SES surface #7.2: minimum, -15.65, mean -1.42, maximum 17.07 To also show corresponding color key, enter the above coulombic command and add key true > hide #7.1 models > hide #7.2 models > show #7.1 models > show #7.2 models > color #!7 bychain > coulombic #!7 Coulombic values for best_model.pdb_B SES surface #7.1: minimum, -15.27, mean -1.39, maximum 14.62 Coulombic values for best_model.pdb_C SES surface #7.2: minimum, -15.65, mean -1.42, maximum 17.07 To also show corresponding color key, enter the above coulombic command and add key true > hide #7.1 models > hide #7.2 models > hide #!7 atoms > hide #!7 cartoons > show #!7 surfaces > hide #7.1 models > show #7.1 models > hide #!7 models > show #6 models > hide #6 models > show #5 models > hide #5 models > show #4 models > hide #4 models > show #3 models > coulombic #3 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for af564_unrelaxed_rank_2_model_5.pdb_B SES surface #3.1: minimum, -19.91, mean -0.94, maximum 12.04 Coulombic values for af564_unrelaxed_rank_2_model_5.pdb_C SES surface #3.2: minimum, -15.68, mean -1.26, maximum 12.23 To also show corresponding color key, enter the above coulombic command and add key true > hide #!3 models > show #2 models > coulombic #2 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for af564_unrelaxed_rank_1_model_2.pdb_B SES surface #2.1: minimum, -15.27, mean -1.39, maximum 14.62 Coulombic values for af564_unrelaxed_rank_1_model_2.pdb_C SES surface #2.2: minimum, -15.65, mean -1.42, maximum 17.07 To also show corresponding color key, enter the above coulombic command and add key true > color bfactor #!2 4470 atoms, 564 residues, 2 surfaces, atom bfactor range 17.3 to 98.8 > mlp #!2 Map values for surface ""af564_unrelaxed_rank_1_model_2.pdb_B SES surface"": minimum -27.01, mean -6.046, maximum 23.08 Map values for surface ""af564_unrelaxed_rank_1_model_2.pdb_C SES surface"": minimum -27.29, mean -6.069, maximum 24.22 To also show corresponding color key, enter the above mlp command and add key true > rainbow #!2 > color #!2 bypolymer > color #!2 bychain > color #!2 byhetero > color #!2 bynucleotide > hide #!2 models > hide #7.1 models > hide #7.2 models AlphaFold prediction finished Results in /Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpintetramer Downloaded prediction file not found: /Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpintetramer/best_model.pdb ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M1 Pro 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: MacBookPro18,3 Model Number: MKGQ3SM/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 8419.80.7 OS Loader Version: 8419.80.7 Software: System Software Overview: System Version: macOS 13.2.1 (22D68) Kernel Version: Darwin 22.3.0 Time since boot: 3 jours, 9 heures et 46 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal 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 Structure Prediction can't reproduce Eric Pettersen all ChimeraX