id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10072 'StrandPlank' object has no attribute '_straight_tilt' samo.lesnik@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-5.4.0-164-generic-x86_64-with-glibc2.31 ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description I tried to make strands in cartoons as planks with the command: cartoon style protein modeS plank. Log: > select @area Nothing selected > select @area 5 Expected a keyword > select @alt_loc Nothing selected > select @alt_loc=A Expected an objects specifier or a keyword > select @\alt_loc=A Expected an objects specifier or a keyword > select \@alt_loc=A Expected an objects specifier or a keyword > select /@alt_loc=A Expected an objects specifier or a keyword > select @/alt_loc=A Expected an objects specifier or a keyword > select @@alt_loc=A Nothing selected > select @@charge Nothing selected > select @@charge>2 Nothing selected > select @@charge>0 Nothing selected > select @@charge>-1 Nothing selected > select @@idatm_type=Car 724 atoms, 684 bonds, 125 residues, 1 model selected > select @@segname Nothing selected > select @@segname=PROA Nothing selected > select @@segname=A Nothing selected > select @@segname=proa Nothing selected > select ::segname=proa Nothing selected > select ::segname=PROA Nothing selected > select ##segname=PROA Nothing selected > select @@segname=GPRA Nothing selected > select @@segname=MUOR Nothing selected > select ::segname=MUOR Nothing selected > select ##segname=MUOR Nothing selected > select ##segment=MUOR Nothing selected > select ::segment=MUOR Nothing selected > select @@segment=MUOR Nothing selected > select ::segment=MUOR Nothing selected > select ::segment=MUOR Nothing selected > select ::segment=* Nothing selected > select ::segname=* Nothing selected > select @@segname=* Nothing selected > select @@segment=* Nothing selected > select ::segment=* Nothing selected > select ##segment=* Nothing selected > select ##segname=* Nothing selected > select ::segname=* Nothing selected > select ##segname=* Nothing selected > select clear [Repeated 1 time(s)] > select add /?:217 178 atoms, 172 bonds, 5 residues, 1 model selected > select add /?:212 365 atoms, 355 bonds, 10 residues, 1 model selected > select up 745 atoms, 741 bonds, 34 residues, 1 model selected > select clear Drag select of 5 residues > select up 190 atoms, 189 bonds, 12 residues, 1 model selected > hide sel cartoons > select clear Drag select of 15 atoms, 54 residues, 20 bonds > select up 717 atoms, 717 bonds, 43 residues, 2 models selected > select up 737 atoms, 739 bonds, 43 residues, 2 models selected > select up 971 atoms, 973 bonds, 57 residues, 2 models selected > select up 5652 atoms, 5701 bonds, 352 residues, 2 models selected > select clear Drag select of 9 residues > select up 304 atoms, 302 bonds, 20 residues, 1 model selected > select up 5063 atoms, 5110 bonds, 335 residues, 1 model selected > select clear > save /home/samo/vol/opioid_dynamics/forFigures/whole_system.cxs > select clear > select protein 16306 atoms, 16465 bonds, 1028 residues, 1 model selected > select protein zr<3.5 Expected a keyword > select protein 16306 atoms, 16465 bonds, 1028 residues, 1 model selected > select sel :< 3.5 & ~sel 12304 atoms, 10236 bonds, 2058 residues, 1 model selected > select sel :< 3.5 & ~sel 30759 atoms, 27704 bonds, 3780 residues, 1 model selected > select intersect ::name=""TIP"" 8655 atoms, 5770 bonds, 2885 residues, 1 model selected > show sel atoms > style sel stick Changed 8655 atom styles > style sel ball Changed 8655 atom styles > select clear > save /home/samo/vol/opioid_dynamics/forFigures/whole_system.cxs > select clear > select :MOR|:GDP 81 atoms, 87 bonds, 2 residues, 1 model selected > show sel surfaces > style sel sphere Changed 81 atom styles > hide sel surfaces > select clear > save /home/samo/vol/opioid_dynamics/forFigures/whole_system.cxs > select :POPC 54672 atoms, 53756 bonds, 408 residues, 1 model selected > show sel surfaces > select :POPC 54672 atoms, 53756 bonds, 408 residues, 1 model selected > hide sel surfaces > show sel surfaces > clip front 1 axis z position :MOR > ~clip > clip front 5 axis z position :MOR > clip front 3 axis z position :MOR > ~clip > hide sel surfaces > clip front 3 axis z position :MOR > ~clip > clip front 0 axis z position :MOR [Repeated 1 time(s)] > ~clip > clip front 0 axis z position :MOR > ~clip > clip front 0.5 axis z position :MOR > ~clip > clip front -0.5 axis z position :MOR > ~clip > clip front -1.5 axis z position :MOR > ~clip > clip front -2.5 axis z position :MOR [Repeated 3 time(s)] > clip front -3.5 axis z position :MOR > clip front -4.5 axis z position :MOR > save /home/samo/vol/opioid_dynamics/forFigures/whole_system.cxs > clip model #!protein false Missing or invalid ""models"" argument: invalid models specifier > clip #protein false Expected a keyword > clip protein false Expected a keyword > clip plane Expected a keyword > clip plane x Expected a keyword > clip axis z > ~clip > ~clip !protein Expected fewer arguments > clip near Missing ""near"" keyword's argument > clip near plane Invalid ""near"" argument: Expected 'off' or a number > clip near 5 [Repeated 4 time(s)] > ~clip [Repeated 1 time(s)] > clip position :MOR [Repeated 2 time(s)] > clip position :MOR offset Expected a keyword > clip position :MOR offset 5 Expected a keyword > clip model !protein position :MOR Missing or invalid ""models"" argument: invalid models specifier > clip model !protein True position :MOR Missing or invalid ""models"" argument: invalid models specifier > clip model #1!protein True position :MOR Missing or invalid ""models"" argument: only initial part ""#1"" of atom specifier valid > clip model #0!protein True position :MOR Missing or invalid ""models"" argument: only initial part ""#0"" of atom specifier valid > clip model #0 true position :MOR Expected a keyword > clip model #0 true > clip model #0!proteinž true Missing or invalid ""models"" argument: only initial part ""#0"" of atom specifier valid > clip model #0!protein true Missing or invalid ""models"" argument: only initial part ""#0"" of atom specifier valid > clip model #0protein true Missing or invalid ""models"" argument: only initial part ""#0"" of atom specifier valid > clip model #0&protein true > clip model #0&!protein true Missing or invalid ""models"" argument: only initial part ""#0"" of atom specifier valid > clip model #0&protein true > clip model #0&protein false > ~clip > clip model #0&protein false > clip model #0&protein true > ~clip > clip plane z position :MOR Expected a keyword > clip axis z position :MOR [Repeated 3 time(s)] > clip axis z position :MOR offset Expected a keyword > clip axis z position :MOR offset on Expected a keyword > clip axis z position :MOR offset 2 Expected a keyword > clip model protein false > clip axis z position :MOR [Repeated 1 time(s)] > select !protien Expected an objects specifier or a keyword > select not protien Expected an objects specifier or a keyword > select ~protien Expected an objects specifier or a keyword > select protien Expected an objects specifier or a keyword > select protein 16306 atoms, 16465 bonds, 1028 residues, 1 model selected > select protein 16306 atoms, 16465 bonds, 1028 residues, 1 model selected > select !protein Expected an objects specifier or a keyword > select protein 16306 atoms, 16465 bonds, 1028 residues, 1 model selected > select ~protein 307721 atoms, 223248 bonds, 84113 residues, 1 model selected > clip protein ~protein Expected a keyword > split protein ~protein Expected a keyword > split atoms protein atoms ~protein Split step5_input.pdb (#1) into 2 models Chain information for step5_input.pdb 1 #1.1 --- Chain | Description ? | No description available > save /home/samo/vol/opioid_dynamics/forFigures/whole_system.cxs > interfaces ~solvent 1 buried areas: #1.2/ #1.1/ 8014 > interfaces ~solvent 1 buried areas: #1.2/ #1.1/ 8014 > ui mousemode right clip [Repeated 1 time(s)] > ui tool show ""Model Panel"" > hide #1.1 models > show #1.1 models > hide #1.2 models > show #1.2 models > clip #1.2 Expected a keyword > clip model #1.2 Model #1.2 clipping True > clip axis y > clip model #1.2 Model #1.2 clipping True > clip model #1.1 false > close session > open /home/samo/vol/opioid_dynamics/M_D_S/namd/step5_input.pdb format pdb Summary of feedback from opening /home/samo/vol/opioid_dynamics/M_D_S/namd/step5_input.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 224022 messages similar to the above omitted Chain information for step5_input.pdb #1 --- Chain | Description ? | No description available > clip > ~clip > split atoms protein|:MOR|:GDP atoms :POPC|:TIP Split step5_input.pdb (#1) into 3 models Chain information for step5_input.pdb 1 #1.1 --- Chain | Description ? | No description available > hide #1.1 models > show #1.1 models > hide #1.3 models > hide #1.2 models > hide #1.1 models > show #1.1 models > hide #1.1 cartoons > hide #1.1 surfaces > hide #1.1 atoms > show #1.1 cartoons > hide #1.1 models > show #1.2 models > hide #1.2 models > show #1.3 models > hide #1.3 models > show #1.1 models > select :MOR|:GDP 81 atoms, 87 bonds, 2 residues, 1 model selected > show sel atoms > hide #1.1 models > show #1.1 models > show #1.2 models > hide #1.1 models > show #1.1 models > hide #1.2 models > save /home/samo/vol/opioid_dynamics/forFigures/whole_system.cxs > style sel sphere Changed 81 atom styles > select clear > select add #1.2 304299 atoms, 220174 bonds, 83617 residues, 1 model selected > select subtract #1.2 Nothing selected > show #1.2 models > hide #1.2 models > show #1.2 models > select TIP Expected an objects specifier or a keyword > select :TIP 249627 atoms, 166418 bonds, 83209 residues, 1 model selected > hide sel atoms > ui mousemode right clip > hide #1.2 models > show #1.2 models > clip model #1.1 false > ui mousemode right clip > hide #1.2 models > show #1.2 models > select :SOD 226 atoms, 226 residues, 1 model selected > select :SOD|:CLA|CHLO Expected an objects specifier or a keyword > select :SOD|:CLA|:CHLO 454 atoms, 454 residues, 1 model selected > select :SOD|:CLA|:CHL1 2970 atoms, 2602 bonds, 488 residues, 1 model selected > hide #1.1-2 atoms > show #1.1-2 atoms > select add #1.2/?:271@C217 2971 atoms, 2602 bonds, 489 residues, 2 models selected > select clear > hide #1.2 models > show #1.2 models > hide #1.1 models > show #1.1 models > select clear > hide #1.1-2 atoms > show #1.1-2 atoms > select POPC Expected an objects specifier or a keyword > select :POPC 54672 atoms, 53756 bonds, 408 residues, 1 model selected > hide sel atoms > show sel atoms > style sel stick Changed 54672 atom styles > style sel stick Changed 54672 atom styles > style sel stick Changed 54672 atom styles > style sel stick Changed 54672 atom styles > style sel stick Changed 54672 atom styles > hide sel atoms > show sel surfaces > hide #1.1 models > show #1.1 models > show sel atoms > hide sel atoms > select #1.1 16387 atoms, 16552 bonds, 1030 residues, 1 model selected > hide #!1.2 models > show #!1.2 models > hide #1.1 models > show #1.1 models > hide sel atoms > hide sel cartoons > show sel cartoons > select clear > select TIP Expected an objects specifier or a keyword > select :TIP 249627 atoms, 166418 bonds, 83209 residues, 1 model selected > hide sel atoms > select clear > save /home/samo/vol/opioid_dynamics/forFigures/whole_system.cxs > select :MOR 41 atoms, 45 bonds, 1 residue, 1 model selected > show sel atoms > select :GDP 40 atoms, 42 bonds, 1 residue, 1 model selected > show sel atoms > select clear [Repeated 1 time(s)] > hide #1.1#!1.2 cartoons > show #1.1#!1.2 cartoons > save /home/samo/vol/opioid_dynamics/forFigures/whole_system.cxs > ui mousemode right clip [Repeated 1 time(s)] > clip model #1.1 false > save /home/samo/vol/opioid_dynamics/forFigures/whole_system.cxs > cartoon style pipe helix Expected an atoms specifier or a keyword > cartoon > cartoon style protein mode Expected keyword ""modeHelix"" or ""modeStrand"" > cartoon style protein modeHelix Missing ""modeHelix"" keyword's argument > cartoon style protein modeHelix tube > cartoon style protein modeHelix tube width 1.5 > cartoon style protein modeHelix tube width 1.0 > cartoon style protein modeHelix tube width 1.6 > cartoon style protein modeHelix tube > cartoon style protein modeHelix tube radius 2 > cartoon style protein modeHelix tube radius 2 sides 2 Invalid ""sides"" argument: Must be greater than or equal to 3 > cartoon style protein modeHelix tube radius 2 sides 3 Invalid ""sides"" argument: Expected an even integer > cartoon style protein modeHelix tube radius 2 sides 5 Invalid ""sides"" argument: Expected an even integer > cartoon style protein modeHelix tube radius 2 sides 6 > cartoon style protein modeHelix tube radius 2 > cartoon style protein mode Expected keyword ""modeHelix"" or ""modeStrand"" > cartoon style protein modeStrand Missing ""modeStrand"" keyword's argument > cartoon style protein modeStrand Missing ""modeStrand"" keyword's argument > cartoon style protein modeStrand arrow Invalid ""modeStrand"" argument: Should be one of 'default' or 'plank' > cartoon style protein modeStrand plank 6 oxygens of 105 atoms in 6 residues Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/triggerset.py"", line 138, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 1809, in _update_graphics_if_needed s[i].update_graphics_if_needed() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 347, in update_graphics_if_needed self._create_ribbon_graphics() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 651, in _create_ribbon_graphics ribbons_drawing.compute_ribbons(self) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/atomic/ribbon.py"", line 589, in compute_ribbons _make_ribbon_graphics(structure, self) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/atomic/ribbon.py"", line 118, in _make_ribbon_graphics _smooth_ribbon(residues, coords, guides, helix_ranges, sheet_ranges, File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/atomic/ribbon.py"", line 928, in _smooth_ribbon _arc_strand(rlist, coords, guides, start, end) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/atomic/ribbon.py"", line 1072, in _arc_strand sp = StrandPlank(coords[start:end], oxygens.coords) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/atomic/sse.py"", line 477, in __init__ self._straight_optimize() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/atomic/sse.py"", line 555, in _straight_optimize self.width_vector, self.thickness_vector = self._straight_tilt() AttributeError: 'StrandPlank' object has no attribute '_straight_tilt' Error processing trigger ""graphics update"": AttributeError: 'StrandPlank' object has no attribute '_straight_tilt' File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/atomic/sse.py"", line 555, in _straight_optimize self.width_vector, self.thickness_vector = self._straight_tilt() See log for complete Python traceback. > cartoon style protein step5_input.pdb 1 #1.1 \- helix mode=tube xsection=round width=1.6 height=0.4 arrow=False arrow scale=2 \- strand mode=plank xsection=square width=1.6 height=0.4 arrow=True arrow scale=2 \- coil xsection=round width=0.4 height=0.4 \- nucleic xsection=square width=0.4 height=2 \- divisions=20 \- oval parameters: sides=6 \- barbell parameters: sides=18 scale=0.5 > show #1.1#!1.2 atoms > select clear > show #1.1#!1.2 cartoons > hide #1.1 models > show #1.1 models > select protein 16306 atoms, 16465 bonds, 1028 residues, 1 model selected > show sel cartoons > show sel atoms > show sel cartoons OpenGL version: 3.3.0 NVIDIA 525.125.06 OpenGL renderer: NVIDIA GeForce GTX 1050 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_US.UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=cinnamon XDG_SESSION_DESKTOP=cinnamon XDG_CURRENT_DESKTOP=X-Cinnamon DISPLAY=:0 Manufacturer: System manufacturer Model: System Product Name OS: Linux Mint 20 Ulyana Architecture: 64bit ELF Virtual Machine: none CPU: 12 AMD Ryzen 5 2600X Six-Core Processor Cache Size: 512 KB Memory: total used free shared buff/cache available Mem: 47Gi 10Gi 25Gi 182Mi 11Gi 36Gi Swap: 2.0Gi 0B 2.0Gi Graphics: 08:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP107 [GeForce GTX 1050 Ti] [10de:1c82] (rev a1) Subsystem: Gigabyte Technology Co., Ltd GP107 [GeForce GTX 1050 Ti] [1458:372a] Kernel driver in use: nvidia Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2023.5.7 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 distro: 1.7.0 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 23.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Depiction not a bug all ChimeraX