id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16702 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.2-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/wangxi/Downloads/ChimeraX/RV-VP1/1cn3.cif 1cn3.cif title: Interaction of polyomavirus internal protein VP2 with major capsid protein VP1 and implications for participation of VP2 In viral entry [more info...] Chain information for 1cn3.cif #1 --- Chain | Description | UniProt A B C D E | COAT PROTEIN VP1 | COA1_POVMP 34-316 F | FRAGMENT OF COAT PROTEIN VP2 | COA2_POVMC 11-29 1cn3.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| software_defined_assembly > sequence chain #1/A#1/B#1/C#1/D#1/E Alignment identifier is 1 > set bgColor white > lighting simple > lighting soft > lighting full > style ball Changed 11261 atom styles > style sphere Changed 11261 atom styles > style stick Changed 11261 atom styles > style stick Changed 11261 atom styles > style stick Changed 11261 atom styles > hide cartoons > show cartoons > show atoms > ui tool show ""Selection Inspector"" > color bfactor 11261 atoms, 1444 residues, atom bfactor range 2 to 97.2 > hbonds reveal true 1301 hydrogen bonds found > ~hbonds > interfaces ~solvent 7 buried areas: C D 2242, A E 2238, B C 2237, A B 2235, D E 2231, A F 493, E F 470 Alignment identifier is 2 Alignment identifier is 1/F > hbonds reveal true 1301 hydrogen bonds found > color bfactor 11261 atoms, 1444 residues, atom bfactor range 2 to 97.2 > mlp Map values for surface ""1cn3.cif_A SES surface"": minimum -31.84, mean -4.97, maximum 22.19 Map values for surface ""1cn3.cif_B SES surface"": minimum -32.77, mean -4.877, maximum 23.77 Map values for surface ""1cn3.cif_C SES surface"": minimum -32.41, mean -4.922, maximum 22.74 Map values for surface ""1cn3.cif_D SES surface"": minimum -32.77, mean -4.929, maximum 22.55 Map values for surface ""1cn3.cif_E SES surface"": minimum -32.85, mean -4.922, maximum 23.04 Map values for surface ""1cn3.cif_F SES surface"": minimum -26.55, mean -4.701, maximum 21.6 To also show corresponding color key, enter the above mlp command and add key true > mlp Map values for surface ""1cn3.cif_A SES surface"": minimum -31.84, mean -4.97, maximum 22.19 Map values for surface ""1cn3.cif_B SES surface"": minimum -32.77, mean -4.877, maximum 23.77 Map values for surface ""1cn3.cif_C SES surface"": minimum -32.41, mean -4.922, maximum 22.74 Map values for surface ""1cn3.cif_D SES surface"": minimum -32.77, mean -4.929, maximum 22.55 Map values for surface ""1cn3.cif_E SES surface"": minimum -32.85, mean -4.922, maximum 23.04 Map values for surface ""1cn3.cif_F SES surface"": minimum -26.55, mean -4.701, maximum 21.6 To also show corresponding color key, enter the above mlp command and add key true > coulombic The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: /F GLY 29 OXT Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 1cn3.cif_A SES surface #1.2: minimum, -20.00, mean -2.15, maximum 10.59 Coulombic values for 1cn3.cif_B SES surface #1.3: minimum, -17.68, mean -2.14, maximum 10.47 Coulombic values for 1cn3.cif_C SES surface #1.4: minimum, -15.92, mean -2.16, maximum 10.57 Coulombic values for 1cn3.cif_D SES surface #1.5: minimum, -20.26, mean -2.17, maximum 10.62 Coulombic values for 1cn3.cif_E SES surface #1.6: minimum, -16.32, mean -2.15, maximum 10.27 Coulombic values for 1cn3.cif_F SES surface #1.7: minimum, -10.58, mean -0.11, maximum 9.53 To also show corresponding color key, enter the above coulombic command and add key true > coulombic Coulombic values for 1cn3.cif_A SES surface #1.2: minimum, -20.00, mean -2.15, maximum 10.59 Coulombic values for 1cn3.cif_B SES surface #1.3: minimum, -17.68, mean -2.14, maximum 10.47 Coulombic values for 1cn3.cif_C SES surface #1.4: minimum, -15.92, mean -2.16, maximum 10.57 Coulombic values for 1cn3.cif_D SES surface #1.5: minimum, -20.26, mean -2.17, maximum 10.62 Coulombic values for 1cn3.cif_E SES surface #1.6: minimum, -16.32, mean -2.15, maximum 10.27 Coulombic values for 1cn3.cif_F SES surface #1.7: minimum, -10.58, mean -0.11, maximum 9.53 To also show corresponding color key, enter the above coulombic command and add key true > rainbow > color bypolymer > color bynucleotide > color byhetero > color bychain > color bypolymer > rainbow > style stick Changed 11261 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > style ball Changed 11261 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > hbonds reveal true 1301 hydrogen bonds found > ~hbonds > rainbow > open /Users/wangxi/Downloads/ChimeraX/RV-VP1/1fpn.cif Summary of feedback from opening /Users/wangxi/Downloads/ChimeraX/RV- VP1/1fpn.cif --- note | Fetching CCD DAO from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/DAO/DAO.cif 1fpn.cif title: Human rhinovirus serotype 2 (HRV2) [more info...] Chain information for 1fpn.cif #2 --- Chain | Description | UniProt 1 | COAT PROTEIN VP1 | POLG_HRV2 1-289 2 | COAT PROTEIN VP2 | POLG_HRV2 1-261 3 | COAT PROTEIN VP3 | POLG_HRV2 1-237 4 | COAT PROTEIN VP4 | POLG_HRV2 1-68 Non-standard residues in 1fpn.cif #2 --- DAO — lauric acid 1fpn.cif mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame 6| crystal asymmetric unit, crystal frame > color byhetero > color bychain > color bypolymer > hide #!1 models > show target m > hide #!1 models > close #1 > close #2 > show # target m Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > close # Expected a models specifier or a keyword > open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/1fpn-HRV2.pdb 1fpn-HRV2.pdb title: Human rhinovirus serotype 2 (HRV2) [more info...] Chain information for 1fpn-HRV2.pdb #1 --- Chain | Description | UniProt 1 | coat protein VP1 | POLG_HRV2 1-289 2 | coat protein VP2 | POLG_HRV2 1-261 3 | coat protein VP3 | POLG_HRV2 1-237 4 | coat protein VP4 | POLG_HRV2 1-68 Non-standard residues in 1fpn-HRV2.pdb #1 --- DAO — lauric acid > show atoms > hide atoms > show cartoons > hide cartoons > show cartoons > style stick Changed 6316 atom styles > style sphere Changed 6316 atom styles > style sphere Changed 6316 atom styles > style ball Changed 6316 atom styles > set bgColor white > set bgColor black > lighting simple > lighting soft > lighting full > color byhetero > color bychain > color bypolymer > nucleotides atoms > style nucleic stick Changed 0 atom styles > lighting simple > ui tool show ""Side View"" > transparency 50 > volume showOutlineBox true No volumes specified > volume style mesh No volumes specified > volume style surface No volumes specified > volume style surface No volumes specified > volume style surface No volumes specified Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic models, 0 maps. Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 0 maps. Hide dust shortcut requires a displayed map surface Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic models, 0 maps. > color bynucleotide > show surfaces > show cartoons > show atoms > nucleotides atoms > style nucleic stick Changed 0 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > style stick Changed 6316 atom styles > style stick Changed 6316 atom styles > style sphere Changed 6316 atom styles > style ball Changed 6316 atom styles > color bynucleotide > color byhetero > color bychain > color byhetero > color bychain > color bypolymer > rainbow > coulombic The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /1 SER 133 /2 ARG 12 /4 GLN 7 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 1fpn-HRV2.pdb_1 SES surface #1.2: minimum, -13.40, mean -0.31, maximum 15.27 Coulombic values for 1fpn-HRV2.pdb_2 SES surface #1.3: minimum, -13.04, mean -0.93, maximum 9.96 Coulombic values for 1fpn-HRV2.pdb_3 SES surface #1.4: minimum, -13.61, mean -1.20, maximum 8.60 Coulombic values for 1fpn-HRV2.pdb_4 SES surface #1.5: minimum, -5.82, mean 0.95, maximum 8.35 To also show corresponding color key, enter the above coulombic command and add key true > mlp Map values for surface ""1fpn-HRV2.pdb_1 SES surface"": minimum -28.4, mean -4.591, maximum 23.44 Map values for surface ""1fpn-HRV2.pdb_2 SES surface"": minimum -31.93, mean -5.269, maximum 22.54 Map values for surface ""1fpn-HRV2.pdb_3 SES surface"": minimum -26.51, mean -4.189, maximum 21.95 Map values for surface ""1fpn-HRV2.pdb_4 SES surface"": minimum -22.89, mean -4.832, maximum 21.79 To also show corresponding color key, enter the above mlp command and add key true > mlp Map values for surface ""1fpn-HRV2.pdb_1 SES surface"": minimum -28.4, mean -4.591, maximum 23.44 Map values for surface ""1fpn-HRV2.pdb_2 SES surface"": minimum -31.93, mean -5.269, maximum 22.54 Map values for surface ""1fpn-HRV2.pdb_3 SES surface"": minimum -26.51, mean -4.189, maximum 21.95 Map values for surface ""1fpn-HRV2.pdb_4 SES surface"": minimum -22.89, mean -4.832, maximum 21.79 To also show corresponding color key, enter the above mlp command and add key true > color bfactor 6316 atoms, 941 residues, 4 surfaces, atom bfactor range 8.1 to 100 > hbonds reveal true 1092 hydrogen bonds found > show atoms > interfaces ~solvent 5 buried areas: 1 3 4025, 1 2 1983, 2 3 1628, 3 4 371, 1 4 354 Alignment identifier is 1/1 Alignment identifier is 1/2 Alignment identifier is 1/3 Alignment identifier is 1/4 > select clear > ui tool show ""Selection Inspector"" > select > /1:34-35,75-83,94-98,114-131,140-146,168-172,179-182,191-192,215-220,229-247 650 atoms, 663 bonds, 65 pseudobonds, 77 residues, 2 models selected > select /1:36-40,46-51,62-72,104-112,158-163 301 atoms, 302 bonds, 25 pseudobonds, 37 residues, 2 models selected > select /1:34 8 atoms, 7 bonds, 1 residue, 1 model selected > select /1:34-41 56 atoms, 56 bonds, 3 pseudobonds, 8 residues, 2 models selected > select /1:28 6 atoms, 5 bonds, 1 residue, 1 model selected > select /1:28-43 106 atoms, 107 bonds, 5 pseudobonds, 16 residues, 2 models selected > movie record > turn y 2 180 > wait 180 > movie encode /Users/wangxi/Desktop/movie1.mp4 Movie saved to /Users/wangxi/Desktop/movie1.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/wangxi/Desktop/movie2.mp4 Movie saved to /Users/wangxi/Desktop/movie2.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/wangxi/Desktop/movie3.mp4 Movie saved to /Users/wangxi/Desktop/movie3.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/wangxi/Desktop/movie4.mp4 Movie saved to /Users/wangxi/Desktop/movie4.mp4 > save /Users/wangxi/Desktop/image1.png supersample 3 > show sel cartoons > hide sel cartoons > style sel stick Changed 106 atom styles > style sel sphere Changed 106 atom styles > style sel ball Changed 106 atom styles > color bfactor sel 106 atoms, 16 residues, 1 surfaces, atom bfactor range 64.8 to 98.6 > hbonds sel reveal true 16 hydrogen bonds found > ~hbonds > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > color bfactor sel 106 atoms, 16 residues, 1 surfaces, atom bfactor range 64.8 to 98.6 > mlp sel Map values for surface ""1fpn-HRV2.pdb_1 SES surface"": minimum -28.4, mean -4.591, maximum 23.44 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for 1fpn-HRV2.pdb_1 SES surface #1.2: minimum, -13.40, mean -0.31, maximum 15.27 To also show corresponding color key, enter the above coulombic command and add key true > rainbow sel > color sel bypolymer > color sel bychain > color sel byhetero > color sel bynucleotide > style sel stick Changed 106 atom styles > style sel stick Changed 106 atom styles > style sel sphere Changed 106 atom styles > set bgColor white > set bgColor black > set bgColor white > lighting simple > lighting soft > lighting full > show sel atoms > hide sel atoms > show sel cartoons > hide sel cartoons > style sel stick Changed 106 atom styles > set bgColor white > color sel byhetero > style sel ball Changed 106 atom styles > color sel bynucleotide > color sel bychain > color sel bypolymer > rainbow sel > coulombic sel Coulombic values for 1fpn-HRV2.pdb_1 SES surface #1.2: minimum, -13.40, mean -0.31, maximum 15.27 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for 1fpn-HRV2.pdb_1 SES surface #1.2: minimum, -13.40, mean -0.31, maximum 15.27 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for 1fpn-HRV2.pdb_1 SES surface #1.2: minimum, -13.40, mean -0.31, maximum 15.27 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""1fpn-HRV2.pdb_1 SES surface"": minimum -28.4, mean -4.591, maximum 23.44 To also show corresponding color key, enter the above mlp command and add key true > color bfactor sel 106 atoms, 16 residues, 1 surfaces, atom bfactor range 64.8 to 98.6 > hbonds sel reveal true 16 hydrogen bonds found > hbonds sel reveal true 16 hydrogen bonds found > ~hbonds Destroying pre-existing alignment with identifier 1/1 Alignment identifier is 1/1 > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel cartoons > hide sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > hide sel surfaces > hide sel cartoons > hide sel atoms > style sel stick Changed 2168 atom styles > style sel stick Changed 2168 atom styles > style sel sphere Changed 2168 atom styles > style sel ball Changed 2168 atom styles > select /1:23 6 atoms, 5 bonds, 1 residue, 1 model selected > select /1:23-43 141 atoms, 143 bonds, 21 residues, 1 model selected > select /1:23 6 atoms, 5 bonds, 1 residue, 1 model selected > select /1:23-43 141 atoms, 143 bonds, 21 residues, 1 model selected > ~hbonds > show sel surfaces > show sel cartoons > show sel atoms > color sel byhetero > color sel bychain > color sel bypolymer > rainbow sel > coulombic sel Coulombic values for 1fpn-HRV2.pdb_1 SES surface #1.2: minimum, -13.40, mean -0.31, maximum 15.27 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""1fpn-HRV2.pdb_1 SES surface"": minimum -28.4, mean -4.591, maximum 23.44 To also show corresponding color key, enter the above mlp command and add key true > color bfactor sel 141 atoms, 21 residues, 1 surfaces, atom bfactor range 64.8 to 98.6 > color bfactor sel 141 atoms, 21 residues, 1 surfaces, atom bfactor range 64.8 to 98.6 > hbonds sel reveal true 19 hydrogen bonds found > ~hbonds Destroying pre-existing alignment with identifier 1/1 Alignment identifier is 1/1 > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > nucleotides sel slab > style nucleic & sel stick Changed 0 atom styles > color sel bynucleotide > set bgColor white > lighting simple > lighting soft > volume region all imageMode ""full region"" No volumes specified > volume style mesh No volumes specified > volume style mesh No volumes specified > volume style surface No volumes specified > volume style surface No volumes specified > volume hide No volumes specified > volume hide No volumes specified > volume showOutlineBox true No volumes specified > transparency sel 50 > transparency sel 0 > volume step 1 No volumes specified > volume planes z style image imageMode ""full region"" No volumes specified Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic models, 0 maps. Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 0 maps. > ui mousemode right ""mark maximum"" > style sel ball Changed 141 atom styles > style sel ball Changed 141 atom styles > rainbow sel > open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/1fpn-HRV2.pdb 1fpn-HRV2.pdb title: Human rhinovirus serotype 2 (HRV2) [more info...] Chain information for 1fpn-HRV2.pdb #2 --- Chain | Description | UniProt 1 | coat protein VP1 | POLG_HRV2 1-289 2 | coat protein VP2 | POLG_HRV2 1-261 3 | coat protein VP3 | POLG_HRV2 1-237 4 | coat protein VP4 | POLG_HRV2 1-68 Non-standard residues in 1fpn-HRV2.pdb #2 --- DAO — lauric acid > show sel atoms > hide sel atoms > show sel cartoons > hide sel cartoons > open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/1fpn-HRV2.pdb format pdb 1fpn-HRV2.pdb title: Human rhinovirus serotype 2 (HRV2) [more info...] Chain information for 1fpn-HRV2.pdb #3 --- Chain | Description | UniProt 1 | coat protein VP1 | POLG_HRV2 1-289 2 | coat protein VP2 | POLG_HRV2 1-261 3 | coat protein VP3 | POLG_HRV2 1-237 4 | coat protein VP4 | POLG_HRV2 1-68 Non-standard residues in 1fpn-HRV2.pdb #3 --- DAO — lauric acid > show sel atoms > hide sel atoms > open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/1fpn-HRV2.pdb format pdb 1fpn-HRV2.pdb title: Human rhinovirus serotype 2 (HRV2) [more info...] Chain information for 1fpn-HRV2.pdb #4 --- Chain | Description | UniProt 1 | coat protein VP1 | POLG_HRV2 1-289 2 | coat protein VP2 | POLG_HRV2 1-261 3 | coat protein VP3 | POLG_HRV2 1-237 4 | coat protein VP4 | POLG_HRV2 1-68 Non-standard residues in 1fpn-HRV2.pdb #4 --- DAO — lauric acid > open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/1fpn-HRV2.pdb format pdb 1fpn-HRV2.pdb title: Human rhinovirus serotype 2 (HRV2) [more info...] Chain information for 1fpn-HRV2.pdb #5 --- Chain | Description | UniProt 1 | coat protein VP1 | POLG_HRV2 1-289 2 | coat protein VP2 | POLG_HRV2 1-261 3 | coat protein VP3 | POLG_HRV2 1-237 4 | coat protein VP4 | POLG_HRV2 1-68 Non-standard residues in 1fpn-HRV2.pdb #5 --- DAO — lauric acid > transparency sel 50 > volume style image No volumes specified > volume style mesh No volumes specified > volume style mesh No volumes specified > volume style image No volumes specified > transparency sel 0 > volume showOutlineBox true No volumes specified > volume step 1 No volumes specified > volume region all imageMode ""full region"" No volumes specified Color zone shortcut requires 1 displayed atomic model and 1 map, got 5 atomic models, 0 maps. > volume hide No volumes specified > color sel bynucleotide > color sel byhetero > select backbone 15630 atoms, 15605 bonds, 5 pseudobonds, 3905 residues, 10 models selected > undo > ui tool show AlphaFold > select clear > select #1/1:23 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/1:23-43 141 atoms, 143 bonds, 21 residues, 1 model selected > ui tool show ""Basic Actions"" > ui tool show ""Color Key"" > ui mousemode right ""color key"" > ui mousemode right ""mark maximum"" > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/2hwd-HRV1A.pdb 2hwd-HRV1A.pdb title: A comparison of the ANTI-rhinoviral drug binding pocket In HRV14 and HRV1A [more info...] Chain information for 2hwd-HRV1A.pdb #7 --- Chain | Description | UniProt 1 | human rhinovirus 1A coat protein (subunit VP1) | POLG_HRV1A 1-287 2 | human rhinovirus 1A coat protein (subunit VP2) | POLG_HRV1A 1-263 3 | human rhinovirus 1A coat protein (subunit VP3) | POLG_HRV1A 1-238 4 | human rhinovirus 1A coat protein (subunit VP4) | POLG_HRV1A 1-44 Non-standard residues in 2hwd-HRV1A.pdb #7 --- W91 — 5-(3-(2,6-dichloro-4-(4,5-dihydro-2-oxazolyl)phenoxy)propyl)-3-methyl isoxazole (WIN56291) > close session > open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/2hwd-HRV1A.pdb format pdb 2hwd-HRV1A.pdb title: A comparison of the ANTI-rhinoviral drug binding pocket In HRV14 and HRV1A [more info...] Chain information for 2hwd-HRV1A.pdb #1 --- Chain | Description | UniProt 1 | human rhinovirus 1A coat protein (subunit VP1) | POLG_HRV1A 1-287 2 | human rhinovirus 1A coat protein (subunit VP2) | POLG_HRV1A 1-263 3 | human rhinovirus 1A coat protein (subunit VP3) | POLG_HRV1A 1-238 4 | human rhinovirus 1A coat protein (subunit VP4) | POLG_HRV1A 1-44 Non-standard residues in 2hwd-HRV1A.pdb #1 --- W91 — 5-(3-(2,6-dichloro-4-(4,5-dihydro-2-oxazolyl)phenoxy)propyl)-3-methyl isoxazole (WIN56291) Alignment identifier is 1/1 Alignment identifier is 1/2 Alignment identifier is 1/3 Alignment identifier is 1/4 > select /1:43-44 14 atoms, 13 bonds, 2 residues, 1 model selected > select /1:42-44 21 atoms, 20 bonds, 3 residues, 1 model selected > select /1:28 6 atoms, 5 bonds, 1 residue, 1 model selected > select /1:28-43 109 atoms, 110 bonds, 16 residues, 1 model selected > select clear > select /1:5-287 2262 atoms, 2322 bonds, 283 residues, 1 model selected > select clear > select /4 151 atoms, 154 bonds, 19 residues, 1 model selected > select clear > select /2 1979 atoms, 2033 bonds, 253 residues, 1 model selected > select /3:1 4 atoms, 3 bonds, 1 residue, 1 model selected > select /3 1831 atoms, 1878 bonds, 238 residues, 1 model selected > select clear > select /1:5-287 2262 atoms, 2322 bonds, 283 residues, 1 model selected > select /1:23 6 atoms, 5 bonds, 1 residue, 1 model selected > select /1:23-43 149 atoms, 152 bonds, 21 residues, 1 model selected > view sel > view > view orient > lighting simple > lighting soft > lighting simple > lighting full > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting simple > rainbow sel > movie record > turn y 2 180 > wait 180 > movie encode /Users/wangxi/Desktop/movie1.mp4 Movie saved to /Users/wangxi/Desktop/movie1.mp4 > save /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/2hwd-HRV1A-ribbon.cxs > save /Users/wangxi/Desktop/image2.png supersample 3 > style sel sphere Changed 149 atom styles > style sel sphere Changed 149 atom styles > style sel stick Changed 149 atom styles > style sel ball Changed 149 atom styles > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel atoms > show sel atoms > style sel stick Changed 149 atom styles > style sel sphere Changed 149 atom styles > style sel ball Changed 149 atom styles > style sel stick Changed 149 atom styles > show sel atoms > hide sel atoms > show sel atoms > show sel cartoons > save /Users/wangxi/Desktop/image3.png supersample 3 > select clear > select /1:5-287 2262 atoms, 2322 bonds, 283 residues, 1 model selected > select clear > select /1:5-287 2262 atoms, 2322 bonds, 283 residues, 1 model selected > select /2 1979 atoms, 2033 bonds, 253 residues, 1 model selected > select /4 151 atoms, 154 bonds, 19 residues, 1 model selected > select /4 151 atoms, 154 bonds, 19 residues, 1 model selected > select clear > select /3 1831 atoms, 1878 bonds, 238 residues, 1 model selected > select /3:1 4 atoms, 3 bonds, 1 residue, 1 model selected > select /3:1 4 atoms, 3 bonds, 1 residue, 1 model selected > select clear > select /1:5-287 2262 atoms, 2322 bonds, 283 residues, 1 model selected > select clear > select /4 151 atoms, 154 bonds, 19 residues, 1 model selected > select /3:1 4 atoms, 3 bonds, 1 residue, 1 model selected > select /3 1831 atoms, 1878 bonds, 238 residues, 1 model selected > select clear > select /1:5-287 2262 atoms, 2322 bonds, 283 residues, 1 model selected > lighting simple > lighting soft > lighting simple > set bgColor white > lighting simple > set bgColor white > set bgColor black > set bgColor white > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting simple > hide sel atoms > show sel atoms > style sel stick Changed 2262 atom styles > style sel sphere Changed 2262 atom styles > style sel sphere Changed 2262 atom styles > style sel stick Changed 2262 atom styles > style sel ball Changed 2262 atom styles > style sel ball Changed 2262 atom styles > style sel stick Changed 2262 atom styles > show sel cartoons > hide sel atoms > show sel atoms > hide sel atoms > select /1:23 6 atoms, 5 bonds, 1 residue, 1 model selected > select /1:23-30 60 atoms, 61 bonds, 8 residues, 1 model selected > select /1:28 6 atoms, 5 bonds, 1 residue, 1 model selected > select /1:28-43 109 atoms, 110 bonds, 16 residues, 1 model selected > show sel atoms > style sel stick Changed 109 atom styles > style sel stick Changed 109 atom styles > show sel cartoons > show sel atoms > select clear > select /2 1979 atoms, 2033 bonds, 253 residues, 1 model selected > hide sel cartoons > select /3:1 4 atoms, 3 bonds, 1 residue, 1 model selected > select /3 1831 atoms, 1878 bonds, 238 residues, 1 model selected > hide sel cartoons > select clear > select /2 1979 atoms, 2033 bonds, 253 residues, 1 model selected > hide sel cartoons > select clear > select /4 151 atoms, 154 bonds, 19 residues, 1 model selected > hide sel cartoons > select clear > select /1:5-287 2262 atoms, 2322 bonds, 283 residues, 1 model selected > select /1:28 6 atoms, 5 bonds, 1 residue, 1 model selected > select /1:28-43 109 atoms, 110 bonds, 16 residues, 1 model selected > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > show sel atoms > hide sel atoms > show sel atoms > save /Users/wangxi/Desktop/image4.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/wangxi/Desktop/movie2.mp4 Movie saved to /Users/wangxi/Desktop/movie2.mp4 > select clear > select /2 1979 atoms, 2033 bonds, 253 residues, 1 model selected > select clear > select /2 1979 atoms, 2033 bonds, 253 residues, 1 model selected > select /2:263 9 atoms, 8 bonds, 1 residue, 1 model selected > select /2 1979 atoms, 2033 bonds, 253 residues, 1 model selected > lighting simple > lighting soft > lighting simple > set bgColor white > lighting full > lighting simple > show sel atoms > show sel cartoons > show sel atoms > hide sel atoms > hide sel cartoons > show sel cartoons > save /Users/wangxi/Desktop/image1.png supersample 3 > hide sel cartoons > select /3:1 4 atoms, 3 bonds, 1 residue, 1 model selected > select /3 1831 atoms, 1878 bonds, 238 residues, 1 model selected > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > select clear > select /2 1979 atoms, 2033 bonds, 253 residues, 1 model selected > show sel cartoons > select /3:1 4 atoms, 3 bonds, 1 residue, 1 model selected > select /3 1831 atoms, 1878 bonds, 238 residues, 1 model selected > save /Users/wangxi/Desktop/image1.png supersample 3 > select clear > select /4 151 atoms, 154 bonds, 19 residues, 1 model selected > select /4:44 8 atoms, 7 bonds, 1 residue, 1 model selected > select /4 151 atoms, 154 bonds, 19 residues, 1 model selected > select /4 151 atoms, 154 bonds, 19 residues, 1 model selected > show sel cartoons > save /Users/wangxi/Desktop/image1.png supersample 3 > open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/6sk5-RV-B5.pdb 6sk5-RV-B5.pdb title: Cryo-em structure of rhinovirus-B5 complexed to antiviral obr-5-340 [more info...] Chain information for 6sk5-RV-B5.pdb #2 --- Chain | Description | UniProt A | rhinovirus B5 VP1 | Q7T659_9ENTO 1-288 B | rhinovirus B5 VP2 | B9V433_9ENTO 8-259 C | rhinovirus B5 VP3 | B9V433_9ENTO 1-230 D | rhinovirus B5 VP4 | Q80SQ3_9ENTO 1-69 Non-standard residues in 6sk5-RV-B5.pdb #2 --- LGQ — 6-phenyl-~{N}3-[4-(trifluoromethyl)phenyl]-1~{H}-pyrazolo[3,4-D]pyrimidine-3,4-diamine > open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/6sk5-RV-B5.pdb format pdb 6sk5-RV-B5.pdb title: Cryo-em structure of rhinovirus-B5 complexed to antiviral obr-5-340 [more info...] Chain information for 6sk5-RV-B5.pdb #3 --- Chain | Description | UniProt A | rhinovirus B5 VP1 | Q7T659_9ENTO 1-288 B | rhinovirus B5 VP2 | B9V433_9ENTO 8-259 C | rhinovirus B5 VP3 | B9V433_9ENTO 1-230 D | rhinovirus B5 VP4 | Q80SQ3_9ENTO 1-69 Non-standard residues in 6sk5-RV-B5.pdb #3 --- LGQ — 6-phenyl-~{N}3-[4-(trifluoromethyl)phenyl]-1~{H}-pyrazolo[3,4-D]pyrimidine-3,4-diamine > open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/6sk5-RV-B5.pdb 6sk5-RV-B5.pdb title: Cryo-em structure of rhinovirus-B5 complexed to antiviral obr-5-340 [more info...] Chain information for 6sk5-RV-B5.pdb #4 --- Chain | Description | UniProt A | rhinovirus B5 VP1 | Q7T659_9ENTO 1-288 B | rhinovirus B5 VP2 | B9V433_9ENTO 8-259 C | rhinovirus B5 VP3 | B9V433_9ENTO 1-230 D | rhinovirus B5 VP4 | Q80SQ3_9ENTO 1-69 Non-standard residues in 6sk5-RV-B5.pdb #4 --- LGQ — 6-phenyl-~{N}3-[4-(trifluoromethyl)phenyl]-1~{H}-pyrazolo[3,4-D]pyrimidine-3,4-diamine > close session > open /Users/wangxi/Desktop/Chimera/ChimeraX/PDB/6sk5-RV-B5.pdb format pdb 6sk5-RV-B5.pdb title: Cryo-em structure of rhinovirus-B5 complexed to antiviral obr-5-340 [more info...] Chain information for 6sk5-RV-B5.pdb #1 --- Chain | Description | UniProt A | rhinovirus B5 VP1 | Q7T659_9ENTO 1-288 B | rhinovirus B5 VP2 | B9V433_9ENTO 8-259 C | rhinovirus B5 VP3 | B9V433_9ENTO 1-230 D | rhinovirus B5 VP4 | Q80SQ3_9ENTO 1-69 Non-standard residues in 6sk5-RV-B5.pdb #1 --- LGQ — 6-phenyl-~{N}3-[4-(trifluoromethyl)phenyl]-1~{H}-pyrazolo[3,4-D]pyrimidine-3,4-diamine Alignment identifier is 1/D Alignment identifier is 1/B Alignment identifier is 1/A Alignment identifier is 1/C > select clear > select /A:16-288 4340 atoms, 4399 bonds, 273 residues, 1 model selected > select /A:23-24 23 atoms, 22 bonds, 2 residues, 1 model selected > select /A:23-30 126 atoms, 126 bonds, 8 residues, 1 model selected > select /A:31 16 atoms, 15 bonds, 1 residue, 1 model selected > select /A:31-38 113 atoms, 113 bonds, 8 residues, 1 model selected > select /A:41-42 24 atoms, 23 bonds, 2 residues, 1 model selected > select /A:41-47 99 atoms, 100 bonds, 7 residues, 1 model selected > select /B:8 6 atoms, 5 bonds, 1 residue, 1 model selected > select /B 3826 atoms, 3870 bonds, 252 residues, 1 model selected > hide sel atoms > hide sel cartoons > select /C:1 9 atoms, 8 bonds, 1 residue, 1 model selected > select /C 3583 atoms, 3631 bonds, 230 residues, 1 model selected > hide sel cartoons > select clear > select /D 589 atoms, 595 bonds, 40 residues, 1 model selected > hide sel cartoons > hide sel atoms > hide sel cartoons > select clear > select /A:16-288 4340 atoms, 4399 bonds, 273 residues, 1 model selected > hide sel cartoons > show sel cartoons > select /C:1 9 atoms, 8 bonds, 1 residue, 1 model selected > select /C 3583 atoms, 3631 bonds, 230 residues, 1 model selected > hide sel cartoons > select clear > select /A:16-104 1384 atoms, 1396 bonds, 89 residues, 1 model selected > lighting soft > lighting simple ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,4 Model Number: Z15K0010BLL/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 64 GB System Firmware Version: 11881.61.3 OS Loader Version: 11881.61.3 Software: System Software Overview: System Version: macOS 15.2 (24C101) Kernel Version: Darwin 24.2.0 Time since boot: 1 day, 21 hours, 38 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 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 DELL U2718Q: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported DELL U2718Q: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX