id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14621 Render by Attribute histogram: `bins` must be an integer, a string, or an array goddard@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.3.1-arm64-arm-64bit ChimeraX Version: 1.8.dev202401312028 (2024-01-31 20:28:05 UTC) Description I made a new attribute capsid_radius and render by attribute gave an error trying to show it. Log: UCSF ChimeraX version: 1.8.dev202401312028 (2024-01-31) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open https://www.rbvi.ucsf.edu/chimerax/tutorials.html Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html Compositor returned null texture [Repeated 1 time(s)] Already setting window visible! > open https://www.rbvi.ucsf.edu/chimerax/tutorials.html Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html > open https://www.rbvi.ucsf.edu/chimerax/tutorials.html Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html Compositor returned null texture [Repeated 1 time(s)] Already setting window visible! Compositor returned null texture > open 7rfw 7rfw title: Structure of SARS-CoV-2 main protease in complex with a covalent inhibitor [more info...] Chain information for 7rfw #1 --- Chain | Description | UniProt A | 3C-like proteinase | R1AB_SARS2 1-306 Non-standard residues in 7rfw #1 --- 4WI — (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide (PF-07321332, bound form; nirmatrelvir, bound form; Paxlovid, bound form) 7rfw mmCIF Assemblies --- 1| author_and_software_defined_assembly > style sphere Changed 2574 atom styles > style ball Changed 2574 atom styles > style ball Changed 2574 atom styles > show surfaces > lighting soft > lighting full > lighting soft > set bgColor white > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > save /Users/goddard/Desktop/image1.png supersample 3 > save /Users/goddard/Desktop/test.jpg width 2000 height 1392 supersample 3 > graphics silhouettes false > graphics silhouettes true > ui tool show ""Measure Volume and Area"" > measure buriedarea Missing or invalid ""atoms1"" argument: empty atom specifier > measure buriedarea ligand Missing required ""with_atoms2"" argument > measure buriedarea ligand withAtoms2 protein Buried area between ligand and protein = 444.21 area ligand = 693.91, area protein = 14358, area both = 14163 > ui mousemode right zoom > ui mousemode right rotate > ui mousemode right zoom > hide surfaces > set bgColor black > set bgColor transparent > lighting simple > select ligand 68 atoms, 70 bonds, 1 residue, 1 model selected > style sel stick Changed 68 atom styles > color sel orange > select clear > select /A:401@O4 1 atom, 1 residue, 1 model selected > select /A:401@O4 1 atom, 1 residue, 1 model selected > select up 68 atoms, 70 bonds, 1 residue, 1 model selected > select /A:189@NE2 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > select up 181 atoms, 184 bonds, 24 residues, 2 models selected > select clear > select /A:190@OG1 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 2 models selected > select up 181 atoms, 184 bonds, 24 residues, 2 models selected > select up 2435 atoms, 2491 bonds, 307 residues, 2 models selected > select down 181 atoms, 184 bonds, 24 residues, 2 models selected > select down 7 atoms, 6 bonds, 1 residue, 2 models selected > select down 1 atom, 1 residue, 2 models selected > select down 1 atom, 1 residue, 2 models selected > select down 1 atom, 1 residue, 2 models selected > select down 1 atom, 1 residue, 2 models selected > select down 1 atom, 1 residue, 2 models selected > select down 1 atom, 1 residue, 2 models selected > select :50-60 95 atoms, 96 bonds, 11 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:176-230 440 atoms, 451 bonds, 55 residues, 1 model selected > select /A:176-237 497 atoms, 509 bonds, 62 residues, 1 model selected > select /A:41-43 25 atoms, 25 bonds, 3 residues, 1 model selected > select /A:41-44 31 atoms, 31 bonds, 4 residues, 1 model selected > select /A:10 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:10-15 39 atoms, 38 bonds, 6 residues, 1 model selected > select clear [Repeated 1 time(s)] > select /A:263 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select /A:226 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:226-237 99 atoms, 100 bonds, 12 residues, 1 model selected > select clear > show surfaces > mlp Map values for surface ""7rfw_A SES surface"": minimum -28.17, mean -5.443, maximum 23.64 To also show corresponding color key, enter the above mlp command and add key true > mlp key true Map values for surface ""7rfw_A SES surface"": minimum -28.17, mean -5.443, maximum 23.64 > key lipophilicity :-20 :0 :20 showTool true > ui mousemode right ""color key"" > key pos 0.693536,0.903031 > coulombic The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: /A GLN 306 OXT Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 7rfw_A SES surface #1.1: minimum, -15.70, mean -2.06, maximum 7.67 To also show corresponding color key, enter the above coulombic command and add key true > hide surfaces > hbonds reveal true 635 hydrogen bonds found > ~hbonds > select ligand 68 atoms, 70 bonds, 1 residue, 1 model selected > hbonds sel reveal true 7 hydrogen bonds found > hbonds sel log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 7rfw 7 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A GLY 143 N /A 4WI 401 N5 no hydrogen 2.974 N/A /A HIS 163 NE2 /A 4WI 401 O1 no hydrogen 2.794 N/A /A GLU 166 N /A 4WI 401 O3 no hydrogen 2.823 N/A /A 4WI 401 N1 /A HIS 164 O /A 4WI 401 H1 3.022 2.009 /A 4WI 401 N2 /A GLU 166 OE2 /A 4WI 401 H9 3.202 2.243 /A 4WI 401 N4 /A GLU 166 O /A 4WI 401 H16 2.862 1.924 /A HOH 631 O /A 4WI 401 O4 no hydrogen 3.343 N/A 7 hydrogen bonds found > open 7d6d format pdb fromDatabase pdb 7d6d title: Structural insights INTO membrane remodeling by SNX1 [more info...] Chain information for 7d6d #3 --- Chain | Description | UniProt A B C D E F G H I J K L M N O P | sorting nexin-1 | Q6NZD2_MOUSE 1-521 > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select clear > close #2 > ui mousemode right zoom > hide #!1 models > interfaces #3 & ~solvent 8 buried areas: M N 1704, G H 1704, E F 1704, A B 1704, O P 1704, C D 1704, I J 1704, K L 1704 Already setting window visible! > close #3 > open 7sx3 format mmcif fromDatabase pdb 7sx3 title: Human NALCN-FAM155A-UNC79-UNC80 channelosome with CaM bound, conformation 1/2 [more info...] Chain information for 7sx3 #2 --- Chain | Description | UniProt A | Sodium leak channel non-selective protein,Enhanced green fluorescent protein | NALCN_HUMAN 1-1738, A0A7G8ZY66_MUHV1 1760-2000 B | Transmembrane protein FAM155A | F155A_HUMAN 1-458 C | Calmodulin-1 | CALM1_HUMAN 1-149 D | UNC79,Protein unc-79 homolog,Protein unc-79 homolog | UNC79_HUMAN 174-2635 E | Protein unc-80 homolog | UNC80_HUMAN 1-3258 Non-standard residues in 7sx3 #2 --- 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) PEV — (1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate (phosphatidylethanolamine; 1-palmitoyl-2-oleoyl-Sn- glycero-3-phosphoethanolamine) PGV — (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate (phosphatidylglycerol; 2-vaccenoyl-1-palmitoyl-Sn- glycerol-3-phosphoglycerol) Y01 — cholesterol hemisuccinate > view > interfaces #!2 & ~solvent 6 buried areas: E D 5656, A B 2485, E A 2318, A C 1387, A D 747, E C 514 Already setting window visible! > close #2 > show #!1 models > view > select lig Expected an objects specifier or a keyword > select ligand 68 atoms, 70 bonds, 1 residue, 1 model selected > select sel :< 5 & ~sel 208 atoms, 205 bonds, 27 residues, 1 model selected > color (#!1 & sel) cornflower blue > style sel stick Changed 208 atom styles > select ~sel & ##selected 2366 atoms, 2286 bonds, 7 pseudobonds, 419 residues, 2 models selected > hide sel atoms > show ligand > alias core /A:50-75,100-107@CA > color ::bfactor<30 red > color ::bfactor<70 red > color @@bfactor<30 red > color @@color=orange green > help measure > measure sasa #1 Solvent accessible area for #1 (2574 atoms) = 14028 > color ::area>0 > color ::area=0 > color ::area==0 > color ::area<1 > color ::area>0 blue > select clear > show surfaces > ui tool show ""Render by Attribute"" > color byattribute r:area #!1 target sabc palette > -1.17187e-13,blue:27.1191,white:58.9545,red 2574 atoms, 446 residues, 1 surfaces, atom area range -1.17e-13 to 238 > lighting soft > help list No help found for 'list' > ui tool show ""Render by Attribute"" > help help:user/tools/render.html > help info Already setting window visible! > close session > open 8f76 8f76 title: Human olfactory receptor OR51E2 bound to propionate in complex with miniGs399 [more info...] Chain information for 8f76 #1 --- Chain | Description | UniProt A | Olfactory receptor 51E2 | O51E2_HUMAN 2-320 N | Nanobody 35 | X | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAS2_HUMAN 5-195 204-394 Y | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340 Z | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71 Non-standard residues in 8f76 #1 --- PPI — propanoic acid > select /N:1-126 961 atoms, 981 bonds, 126 residues, 1 model selected > log metadata #1 Metadata for 8f76 #1 --- Title | Human olfactory receptor OR51E2 bound to propionate in complex with miniGs399 Citation | Billesbolle, C.B., de March, C.A., van der Velden, W.J.C., Ma, N., Tewari, J., Del Torrent, C.L., Li, L., Faust, B., Vaidehi, N., Matsunami, H., Manglik, A. (2023). Structural basis of odorant recognition by a human odorant receptor. Nature, 615, 742-749. PMID: 36922591. DOI: 10.1038/s41586-023-05798-y Non-standard residue | PPI — propanoic acid Gene sources | Lama glama Homo sapiens (human) CryoEM Map | EMDB 28896 — open map Experimental method | Electron microscopy Resolution | 3.1Å > open 28896 fromDatabase emdb Opened emdb 28896 as #2, grid size 288,288,288, pixel 0.81, shown at level 0.54, step 2, values float32, fit PDB 8f76 > hide #!1 models > lighting simple > lighting soft > volume #2 step 1 > volume #2 level 2.687 > volume #2 level 0.9636 > volume #2 level 0.949 > volume #2 level 0.7591 > volume #2 level 0.54 > volume #2 level 0.5108 > volume #2 level 0.4962 > volume #2 level 0.467 > volume #2 level 0.4231 > volume #2 level 0.3793 > volume #2 level 0.3647 > volume #2 level 0.3793 > volume #2 level 0.3939 > volume #2 level 1.183 > volume #2 level 0.4962 > volume #2 level 1.519 > volume #2 level 0.6569 > volume #2 level 0.5254 > surface dust #2 size 8.1 > ui tool show AlphaFold Compositor returned null texture [Repeated 1 time(s)] Already setting window visible! > alphafold match O51E2_HUMAN Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json 1 AlphaFold model found using UniProt identifier: Q9H255 (UniProt O51E2_HUMAN) Sequence Similarity --- AlphaFold Model| Query Sequence| Identity %| Coverage % O51E2_HUMAN | O51E2_HUMAN | 100.0 | 100.0 Opened 1 AlphaFold model > ui tool show ""Map Filter"" > volume gaussian #2 sDev 2.03 Opened emdb 28896 gaussian as #4, grid size 288,288,288, pixel 0.81, shown at step 1, values float32 > select #3/A:304 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3/A:60 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:59 12 atoms, 12 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,42.029,0,1,0,49.907,0,0,1,122.66 > view matrix models #3,1,0,0,128.51,0,1,0,75.781,0,0,1,93.994 > view matrix models #3,1,0,0,111.8,0,1,0,99.419,0,0,1,93.884 > view matrix models > #3,0.45847,0.60464,0.65131,107.34,-0.13759,0.77233,-0.62014,109.07,-0.87799,0.1947,0.43729,87.717 > view matrix models > #3,0.45847,0.60464,0.65131,114.95,-0.13759,0.77233,-0.62014,114.21,-0.87799,0.1947,0.43729,86.745 > fitmap #3 inMap #4 Fit molecule AlphaFold O51E2_HUMAN (#3) to map emdb 28896 gaussian (#4) using 2495 atoms average map value = 0.3302, steps = 92 shifted from previous position = 3.14 rotated from previous position = 12.4 degrees atoms outside contour = 1250, contour level = 0.33329 Position of AlphaFold O51E2_HUMAN (#3) relative to emdb 28896 gaussian (#4) coordinates: Matrix rotation and translation 0.48599748 0.45296243 0.74741654 117.11889404 -0.15309820 0.88610724 -0.43746416 113.45066840 -0.86044604 0.09817835 0.49999362 89.86285812 Axis 0.29760469 0.89333358 -0.33672922 Axis point 151.78489123 0.00000000 -10.13003585 Rotation angle (degrees) 64.14792698 Shift along axis 105.94497330 > volume #4 color #ffffb29c > lighting simple > toolshed show Already setting window visible! [Repeated 1 time(s)] > alphafold predict #1/A Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions. Running AlphaFold prediction The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. [Repeated 4 time(s)] > close > open 6c08 | Summary of feedback from opening 6c08 fetched from pdb --- note | Fetching compressed mmCIF 6c08 from http://files.rcsb.org/download/6c08.cif 6c08 title: Zebrafish SLC38A9 with arginine bound in the cytosol open state [more info...] Chain information for 6c08 #1 --- Chain | Description | UniProt A D | antibody Fab Heavy Chain | B E | antibody Fab light chain | C F | Sodium-coupled neutral amino acid transporter 9 | S38A9_DANRE 71-549 Non-standard residues in 6c08 #1 --- ARG — arginine 6c08 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly Already setting window visible! > close > 6co8 Unknown command: 6co8 > open 6co8 Summary of feedback from opening 6co8 fetched from pdb --- note | Fetching compressed mmCIF 6co8 from http://files.rcsb.org/download/6co8.cif 6co8 title: Structure of Zika virus at a resolution of 3.1 Angstrom [more info...] Chain information for 6co8 #1 --- Chain | Description | UniProt A C E | E protein | POLG_ZIKVF 1-504 B D F | M protein | POLG_ZIKVF 1-75 Non-standard residues in 6co8 #1 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose 6co8 mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame > sym #1 assembly 1 Made 60 graphical clones for 6co8 assembly 1 > view > ui tool show ""Side View"" > lighting soft > shape sphere radius 100 > shape sphere radius 300 > close #3 > close #4 > shape sphere radius 200 > hide #3.1 models > lighting simple > show #3.1 models > shape sphere radius 190 modelId #3 > lighting soft > shape sphere radius 190 slab 10 modelId #3 > ui tool show Shell 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. Already setting window visible! [Repeated 1 time(s)] > select @CA 3456 atoms, 3456 residues, 2 models selected > ui tool show ""Render by Attribute"" > save rad.defattr attrName capsid_radius No known/registered attribute capsid_radius > help defattr > setattr sel atoms capsid_radius 0 Assigning capsid_radius attribute to 3456 items Not creating attribute 'capsid_radius'; use 'create true' to override > setattr sel atoms capsid_radius 0 create true Assigning capsid_radius attribute to 3456 items > ui tool show ""Render by Attribute"" Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/numpy/lib/histograms.py"", line 419, in _get_bin_edges n_equal_bins = operator.index(bins) ^^^^^^^^^^^^^^^^^^^^ TypeError: 'float' object cannot be interpreted as an integer The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/render_by_attr/tool.py"", line 333, in _new_attr self._update_histogram(attr_name) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/render_by_attr/tool.py"", line 411, in _update_histogram self.render_histogram.data_source = (min_val, max_val, numpy.histogram( ^^^^^^^^^^^^^^^^ File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/numpy/lib/histograms.py"", line 780, in histogram bin_edges, uniform_bins = _get_bin_edges(a, bins, range, weights) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/numpy/lib/histograms.py"", line 421, in _get_bin_edges raise TypeError( TypeError: `bins` must be an integer, a string, or an array TypeError: `bins` must be an integer, a string, or an array File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/numpy/lib/histograms.py"", line 421, in _get_bin_edges raise TypeError( See log for complete Python traceback. OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,2 Model Number: MK1H3LL/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 10151.81.1 OS Loader Version: 10151.81.1 Software: System Software Overview: System Version: macOS 14.3.1 (23D60) Kernel Version: Darwin 23.3.0 Time since boot: 19 hours, 24 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 32 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.16 alphashape: 1.3.1 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.15 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.3 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.53 ChimeraX-AtomicLibrary: 12.1.4 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.11 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: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8.dev202401312028 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 ChimeraX-DistMonitor: 1.4 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: 1.1.9 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.15 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: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 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 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.2.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11.1 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.15 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: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-TetraScapeCommand: 0.1 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: 1.33.5 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 click: 8.1.7 click-log: 0.4.0 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.43 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.3 MarkupSafe: 2.1.3 matplotlib: 3.8.2 matplotlib-inline: 0.1.6 msgpack: 1.0.7 nest-asyncio: 1.5.9 netCDF4: 1.6.5 networkx: 3.2.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.26.3 openvr: 1.26.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.7 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.3.0 Pygments: 2.16.1 pynmrstar: 3.3.2 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3301 pyparsing: 3.1.1 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.1 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.1 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 Rtree: 1.1.0 scipy: 1.11.4 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.8.1 shapely: 2.0.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 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: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.12.9 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 trimesh: 4.0.8 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Structure Analysis limitation all ChimeraX