id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15320 ChimeraX off screen cdacosta@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.4.1-x86_64-i386-64bit ChimeraX Version: 1.8rc202405202242 (2024-05-20 22:42:21 UTC) Description Had a problem where I cannot resize the ChimeraX window, and cannot grab a corner becuase it is off screen. This is an issue since the command bar is at the bottom of the window. Log: UCSF ChimeraX version: 1.8rc202405202242 (2024-05-20) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/vs7QL6.cxs"" Log from Mon May 27 16:07:17 2024UCSF ChimeraX version: 1.8rc202405202242 (2024-05-20) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/vs7QL6.cxs"" Log from Mon May 27 14:31:24 2024 Startup Messages --- warnings | No presets found in custom preset folder /Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/4 | Misc No presets found in custom preset folder /Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files No presets found in custom preset folder /Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/5 | Tutorials No presets found in custom preset folder /Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/1 | CIF files No presets found in custom preset folder /Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/3 | Scripts 1 messages similar to the above omitted > cd ""/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - > Dropbox/Protein Tools/ChimeraX"" Current working directory is: /Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX UCSF ChimeraX version: 1.8rc202405202242 (2024-05-20) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/1 | CIF files/7ql6.cif"" 7ql6.cif title: Torpedo muscle-type nicotinic acetylcholine receptor - carbamylcholine-bound conformation [more info...] Chain information for 7ql6.cif #1 --- Chain | Description | UniProt A D | Acetylcholine receptor subunit alpha | ACHA_TETCF 1-437 B | Acetylcholine receptor subunit beta | ACHB_TETCF 1-469 C | Acetylcholine receptor subunit delta | ACHD_TETCF 1-501 E | Acetylcholine receptor subunit gamma | ACHG_TETCF 1-489 Non-standard residues in 7ql6.cif #1 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) CCE — 2-[(aminocarbonyl)oxy]-N,N,N-trimethylethanaminium (carbamyl-choline) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) 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 cartoons > lighting soft > graphics silhouettes true > hide #1.1 > open ""/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/AF2 models/Torpedo7QL6_AF2_m1.pdb"" Chain information for Torpedo7QL6_AF2_m1.pdb #2 --- Chain | Description B C | No description available D | No description available E | No description available F | No description available > open ""/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/AF2 models/AncDGE_AF2_m1.pdb"" Chain information for AncDGE_AF2_m1.pdb #3 --- Chain | Description B C | No description available D | No description available E F | No description available > open ""/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/AF2 models/AdultHS_AF2_m4.pdb"" Chain information for AdultHS_AF2_m4.pdb #4 --- Chain | Description B C | No description available D | No description available E | No description available F | No description available > open ""/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/AF2 models/FetalHS_AF2_m1.pdb"" Chain information for FetalHS_AF2_m1.pdb #5 --- Chain | Description B C | No description available D | No description available E | No description available F | No description available > open ""/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/AF2 models/Banc81het_AF2Mod_m9.pdb"" Chain information for Banc81het_AF2Mod_m9.pdb #6 --- Chain | Description A B | No description available C D | No description available E | No description available > hide atoms > show cartoons > lighting soft > graphics silhouettes true > view > select /A:1-433 6596 atoms, 6777 bonds, 1 pseudobond, 818 residues, 3 models selected > select clear > select :CCE 20 atoms, 18 bonds, 2 residues, 1 model selected > show sel surfaces > color (#!1 & sel) red > select clear > save ""/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/vs7QL6.cxs"" > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > save ""/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/vs7QL6.cxs"" ——— End of log from Mon May 27 14:31:24 2024 ——— opened ChimeraX session > ui tool show Matchmaker > matchmaker #2/C#2/D#2/E#2/B#2/F to #1/A#1/B#1/C#1/D#1/E pairing ss > showAlignment true Parameters --- Chain pairing | ss 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 7ql6.cif, chain A (#1) with Torpedo7QL6_AF2_m1.pdb, chain C (#2), sequence alignment score = 2163.8 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: 7ql6.cif #1/A, Torpedo7QL6_AF2_m1.pdb #2/C Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 Matchmaker 7ql6.cif, chain B (#1) with Torpedo7QL6_AF2_m1.pdb, chain D (#2), sequence alignment score = 2280.1 Alignment identifier is 2 Showing conservation header (""seq_conservation"" residue attribute) for alignment 2 Hiding conservation header for alignment 2 Chains used in RMSD evaluation for alignment 2: 7ql6.cif #1/B, Torpedo7QL6_AF2_m1.pdb #2/D Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2 Matchmaker 7ql6.cif, chain C (#1) with Torpedo7QL6_AF2_m1.pdb, chain E (#2), sequence alignment score = 2471.4 Alignment identifier is 3 Showing conservation header (""seq_conservation"" residue attribute) for alignment 3 Hiding conservation header for alignment 3 Chains used in RMSD evaluation for alignment 3: 7ql6.cif #1/C, Torpedo7QL6_AF2_m1.pdb #2/E Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 3 Matchmaker 7ql6.cif, chain D (#1) with Torpedo7QL6_AF2_m1.pdb, chain B (#2), sequence alignment score = 2044.4 Alignment identifier is 4 Showing conservation header (""seq_conservation"" residue attribute) for alignment 4 Hiding conservation header for alignment 4 Chains used in RMSD evaluation for alignment 4: 7ql6.cif #1/D, Torpedo7QL6_AF2_m1.pdb #2/B Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 4 Matchmaker 7ql6.cif, chain E (#1) with Torpedo7QL6_AF2_m1.pdb, chain F (#2), sequence alignment score = 2388.2 Alignment identifier is 5 Showing conservation header (""seq_conservation"" residue attribute) for alignment 5 Hiding conservation header for alignment 5 Chains used in RMSD evaluation for alignment 5: 7ql6.cif #1/E, Torpedo7QL6_AF2_m1.pdb #2/F Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 5 RMSD between 1860 pruned atom pairs is 0.886 angstroms; (across all 1990 pairs: 1.179) > view name p1 > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > view name p1 [Repeated 1 time(s)] > save ""/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/vs7QL6.cxs"" > ui tool show Matchmaker > matchmaker #3/B#3/D#3/F#3/C#3/E to #1/A#1/B#1/C#1/D#1/E pairing ss > showAlignment true Parameters --- Chain pairing | ss 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 7ql6.cif, chain A (#1) with AncDGE_AF2_m1.pdb, chain B (#3), sequence alignment score = 1879.7 Alignment identifier is 6 Showing conservation header (""seq_conservation"" residue attribute) for alignment 6 Hiding conservation header for alignment 6 Chains used in RMSD evaluation for alignment 6: 7ql6.cif #1/A, AncDGE_AF2_m1.pdb #3/B Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 6 Matchmaker 7ql6.cif, chain B (#1) with AncDGE_AF2_m1.pdb, chain D (#3), sequence alignment score = 1520 Alignment identifier is 7 Showing conservation header (""seq_conservation"" residue attribute) for alignment 7 Hiding conservation header for alignment 7 Chains used in RMSD evaluation for alignment 7: 7ql6.cif #1/B, AncDGE_AF2_m1.pdb #3/D Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 7 Matchmaker 7ql6.cif, chain C (#1) with AncDGE_AF2_m1.pdb, chain F (#3), sequence alignment score = 1751.2 Alignment identifier is 8 Showing conservation header (""seq_conservation"" residue attribute) for alignment 8 Hiding conservation header for alignment 8 Chains used in RMSD evaluation for alignment 8: 7ql6.cif #1/C, AncDGE_AF2_m1.pdb #3/F Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 8 Matchmaker 7ql6.cif, chain D (#1) with AncDGE_AF2_m1.pdb, chain C (#3), sequence alignment score = 1777.1 Alignment identifier is 9 Showing conservation header (""seq_conservation"" residue attribute) for alignment 9 Hiding conservation header for alignment 9 Chains used in RMSD evaluation for alignment 9: 7ql6.cif #1/D, AncDGE_AF2_m1.pdb #3/C Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 9 Matchmaker 7ql6.cif, chain E (#1) with AncDGE_AF2_m1.pdb, chain E (#3), sequence alignment score = 1763.7 Alignment identifier is 10 Showing conservation header (""seq_conservation"" residue attribute) for alignment 10 Hiding conservation header for alignment 10 Chains used in RMSD evaluation for alignment 10: 7ql6.cif #1/E, AncDGE_AF2_m1.pdb #3/E Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 10 RMSD between 1835 pruned atom pairs is 0.969 angstroms; (across all 1978 pairs: 1.334) > matchmaker #3/B#3/D#3/F#3/C#3/E to #1/A#1/B#1/C#1/D#1/E pairing ss > showAlignment true Parameters --- Chain pairing | ss 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 7ql6.cif, chain A (#1) with AncDGE_AF2_m1.pdb, chain B (#3), sequence alignment score = 1879.7 Alignment identifier is 11 Showing conservation header (""seq_conservation"" residue attribute) for alignment 11 Hiding conservation header for alignment 11 Chains used in RMSD evaluation for alignment 11: 7ql6.cif #1/A, AncDGE_AF2_m1.pdb #3/B Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 11 Matchmaker 7ql6.cif, chain B (#1) with AncDGE_AF2_m1.pdb, chain D (#3), sequence alignment score = 1520 Alignment identifier is 12 Showing conservation header (""seq_conservation"" residue attribute) for alignment 12 Hiding conservation header for alignment 12 Chains used in RMSD evaluation for alignment 12: 7ql6.cif #1/B, AncDGE_AF2_m1.pdb #3/D Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 12 Matchmaker 7ql6.cif, chain C (#1) with AncDGE_AF2_m1.pdb, chain F (#3), sequence alignment score = 1751.2 Alignment identifier is 13 Showing conservation header (""seq_conservation"" residue attribute) for alignment 13 Hiding conservation header for alignment 13 Chains used in RMSD evaluation for alignment 13: 7ql6.cif #1/C, AncDGE_AF2_m1.pdb #3/F Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 13 Matchmaker 7ql6.cif, chain D (#1) with AncDGE_AF2_m1.pdb, chain C (#3), sequence alignment score = 1777.1 Alignment identifier is 14 Showing conservation header (""seq_conservation"" residue attribute) for alignment 14 Hiding conservation header for alignment 14 Chains used in RMSD evaluation for alignment 14: 7ql6.cif #1/D, AncDGE_AF2_m1.pdb #3/C Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 14 Matchmaker 7ql6.cif, chain E (#1) with AncDGE_AF2_m1.pdb, chain E (#3), sequence alignment score = 1763.7 Alignment identifier is 15 Showing conservation header (""seq_conservation"" residue attribute) for alignment 15 Hiding conservation header for alignment 15 Chains used in RMSD evaluation for alignment 15: 7ql6.cif #1/E, AncDGE_AF2_m1.pdb #3/E Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 15 RMSD between 1835 pruned atom pairs is 0.969 angstroms; (across all 1978 pairs: 1.334) > view name p1 > save ""/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/vs7QL6.cxs"" [Repeated 1 time(s)] > select ~sel & ##selected Nothing selected > view name p2 > view p1 > view p2 > save ""/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/vs7QL6.cxs"" ——— End of log from Mon May 27 16:07:17 2024 ——— opened ChimeraX session > ui tool show Matchmaker > matchmaker #4/C#4/D#4/E#4/B#4/F to #1/A#1/B#1/C#1/D#1/E pairing ss > showAlignment true Parameters --- Chain pairing | ss 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 7ql6.cif, chain A (#1) with AdultHS_AF2_m4.pdb, chain C (#4), sequence alignment score = 1879.7 Alignment identifier is 16 Showing conservation header (""seq_conservation"" residue attribute) for alignment 16 Hiding conservation header for alignment 16 Chains used in RMSD evaluation for alignment 16: 7ql6.cif #1/A, AdultHS_AF2_m4.pdb #4/C Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 16 Matchmaker 7ql6.cif, chain B (#1) with AdultHS_AF2_m4.pdb, chain D (#4), sequence alignment score = 1520 Alignment identifier is 17 Showing conservation header (""seq_conservation"" residue attribute) for alignment 17 Hiding conservation header for alignment 17 Chains used in RMSD evaluation for alignment 17: 7ql6.cif #1/B, AdultHS_AF2_m4.pdb #4/D Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 17 Matchmaker 7ql6.cif, chain C (#1) with AdultHS_AF2_m4.pdb, chain E (#4), sequence alignment score = 1734 Alignment identifier is 18 Showing conservation header (""seq_conservation"" residue attribute) for alignment 18 Hiding conservation header for alignment 18 Chains used in RMSD evaluation for alignment 18: 7ql6.cif #1/C, AdultHS_AF2_m4.pdb #4/E Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 18 Matchmaker 7ql6.cif, chain D (#1) with AdultHS_AF2_m4.pdb, chain B (#4), sequence alignment score = 1777.1 Alignment identifier is 19 Showing conservation header (""seq_conservation"" residue attribute) for alignment 19 Hiding conservation header for alignment 19 Chains used in RMSD evaluation for alignment 19: 7ql6.cif #1/D, AdultHS_AF2_m4.pdb #4/B Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 19 Matchmaker 7ql6.cif, chain E (#1) with AdultHS_AF2_m4.pdb, chain F (#4), sequence alignment score = 1545.5 Alignment identifier is 20 Showing conservation header (""seq_conservation"" residue attribute) for alignment 20 Hiding conservation header for alignment 20 Chains used in RMSD evaluation for alignment 20: 7ql6.cif #1/E, AdultHS_AF2_m4.pdb #4/F Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 20 RMSD between 1773 pruned atom pairs is 1.001 angstroms; (across all 1986 pairs: 1.569) OpenGL version: 4.1 ATI-5.5.17 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 64 GB System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.4222.0.0,0) OS Loader Version: 580~1678 Software: System Software Overview: System Version: macOS 14.4.1 (23E224) Kernel Version: Darwin 23.4.0 Time since boot: 19 minutes, 10 seconds Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2515H: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: RYM1V4CP047L Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Adapter Type: DVI or HDMI Adapter Firmware Version: ff.c8 Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57 ChimeraX-AtomicLibrary: 14.0.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.4 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.4 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: 1.8rc202405202242 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.3 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.16 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.4 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.4 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.51.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.43 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.2 typing-extensions: 4.11.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect closed normal UI limitation Tom Goddard all ChimeraX