id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6117 Color/depth changes based on lighting coyote_v2002@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description I superposed several nearly identical receptors to highlight different position of one sidechain. Probably itcould be done more efficiently, but that's not why I am reporting this. Here's the bug: the color of the protein changes if we sswitch from simple to soft or full lighting. In other words, with different lighting other models emerge as foreground. Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs > format session Log from Wed Feb 9 05:54:01 2022UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs > format session Log from Tue Feb 8 22:40:34 2022UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs > format session Log from Tue Feb 8 18:19:29 2022UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/visvaldas/Documents/work/quinone_reductase/green_red_3nitro_fig.cxs > format session Log from Tue Feb 8 17:22:02 2022UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1qrd2_ref.pdbqt Chain information for 1qrd2_ref.pdb #1 --- Chain | Description A B | No description available Opened 1qrd2_ref.pdbqt containing 1 structures (5369 atoms, 5488 bonds) > open 1qrd2Y128/green_4/FADOx_receptor.pdbqt Chain information for FADOx_receptor.pdb #2 --- Chain | Description A B | No description available Opened FADOx_receptor.pdbqt containing 1 structures (5369 atoms, 5488 bonds) > open 1qrd2/FADOx_receptor.pdbqt Chain information for FADOx_receptor.pdb #3 --- Chain | Description A B | No description available Opened FADOx_receptor.pdbqt containing 1 structures (5369 atoms, 5488 bonds) > open 1qrd2Y128/green_4/3nitroNPDO_ox_docked_1.pdbqt Summary of feedback from opening 1qrd2Y128/green_4/3nitroNPDO_ox_docked_1.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK minimizedAffinity -8.39384747 Ignored bad PDB record found on line 2 REMARK minimizedRMSD -1 Ignored bad PDB record found on line 3 REMARK 1 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C5_5 and N3_20 5 messages similar to the above omitted Opened 3nitroNPDO_ox_docked_1.pdbqt containing 1 structures (22 atoms, 25 bonds) > open 1qrd2Y128/green_4/3nitroPNPDO_ox_docked_1.pdbqt Summary of feedback from opening 1qrd2Y128/green_4/3nitroPNPDO_ox_docked_1.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK minimizedAffinity -8.26599312 Ignored bad PDB record found on line 2 REMARK minimizedRMSD -1 Ignored bad PDB record found on line 3 REMARK 1 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C6_6 and N4_20 5 messages similar to the above omitted Opened 3nitroPNPDO_ox_docked_1.pdbqt containing 1 structures (22 atoms, 25 bonds) > open 1qrd2Y128/green_4/NPDO_ox_docked_1.pdbqt Summary of feedback from opening 1qrd2Y128/green_4/NPDO_ox_docked_1.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK minimizedAffinity -7.901546 Ignored bad PDB record found on line 2 REMARK minimizedRMSD -1 Ignored bad PDB record found on line 3 REMARK 0 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 ROOT 2 messages similar to the above omitted Opened NPDO_ox_docked_1.pdbqt containing 1 structures (19 atoms, 22 bonds) > open 1qrd2Y128/green_4/PNDPO_ox_docked_1.pdbqt Summary of feedback from opening 1qrd2Y128/green_4/PNDPO_ox_docked_1.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK minimizedAffinity -7.76308203 Ignored bad PDB record found on line 2 REMARK minimizedRMSD -1 Ignored bad PDB record found on line 3 REMARK 0 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 ROOT 2 messages similar to the above omitted Opened PNDPO_ox_docked_1.pdbqt containing 1 structures (19 atoms, 22 bonds) > open 1qrd2/3nitroNPDO_ox_docked_1.pdbqt Summary of feedback from opening 1qrd2/3nitroNPDO_ox_docked_1.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK minimizedAffinity -8.51486588 Ignored bad PDB record found on line 2 REMARK minimizedRMSD -1 Ignored bad PDB record found on line 3 REMARK 1 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C5_5 and N3_20 5 messages similar to the above omitted Opened 3nitroNPDO_ox_docked_1.pdbqt containing 1 structures (22 atoms, 25 bonds) > open 1qrd2/3nitroPNPDO_ox_docked_1.pdbqt Summary of feedback from opening 1qrd2/3nitroPNPDO_ox_docked_1.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK minimizedAffinity -8.27984142 Ignored bad PDB record found on line 2 REMARK minimizedRMSD -1 Ignored bad PDB record found on line 3 REMARK 1 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C6_6 and N4_20 5 messages similar to the above omitted Opened 3nitroPNPDO_ox_docked_1.pdbqt containing 1 structures (22 atoms, 25 bonds) > open 1qrd2/NPDO_ox_docked_1.pdbqt Summary of feedback from opening 1qrd2/NPDO_ox_docked_1.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK minimizedAffinity -8.0473671 Ignored bad PDB record found on line 2 REMARK minimizedRMSD -1 Ignored bad PDB record found on line 3 REMARK 0 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 ROOT 2 messages similar to the above omitted Opened NPDO_ox_docked_1.pdbqt containing 1 structures (19 atoms, 22 bonds) > open 1qrd2/PNDPO_ox_docked_1.pdbqt Summary of feedback from opening 1qrd2/PNDPO_ox_docked_1.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK minimizedAffinity -7.86091995 Ignored bad PDB record found on line 2 REMARK minimizedRMSD -1 Ignored bad PDB record found on line 3 REMARK 0 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 ROOT 2 messages similar to the above omitted Opened PNDPO_ox_docked_1.pdbqt containing 1 structures (19 atoms, 22 bonds) > save > /Users/visvaldas/Documents/work/quinone_reductase/green_red_3nitro_fig.cxs > hide #1 models > hide #3 models > hide #4 models > hide #5 models > hide #6 models > hide #7 models > hide #8 models > hide #9 models > hide #10 models > hide #11 models > select #2:128 28 atoms, 28 bonds, 2 residues, 1 model selected > select #2/A:128 14 atoms, 14 bonds, 1 residue, 1 model selected > show sel target ab > select clear > show #3 models > hide #2 models > select #3/A:128 14 atoms, 14 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select H 2853 atoms, 1557 residues, 3 models selected > delete atoms (#3 & sel) > delete bonds (#3 & sel) > select B 6 atoms, 3 residues, 3 models selected > delete atoms (#3 & sel) > delete bonds (#3 & sel) > select clear > save > /Users/visvaldas/Documents/work/quinone_reductase/green_red_3nitro_fig.cxs > show #2 models > show #1 models > select ::name=""FAD"" 176 atoms, 191 bonds, 3 residues, 3 models selected > color sel purple > color sel byhetero > save > /Users/visvaldas/Documents/work/quinone_reductase/green_red_3nitro_fig.cxs > select clear > hide #3 models > hide #2 models > hide #1 models > show #1 models > show #2 models > show #3 models > show #4 models > show #11 models > show #10 models > show #9 models > show #5 models > show #6 models > show #7 models > show #8 models > select H 1902 atoms, 1038 residues, 2 models selected > delete atoms sel > delete bonds sel > select clear > save > /Users/visvaldas/Documents/work/quinone_reductase/green_red_3nitro_fig.cxs [Repeated 1 time(s)] > select #2/A:128@CD1 1 atom, 1 residue, 1 model selected > select up 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel lime > select #3/A:128@CD2 1 atom, 1 residue, 1 model selected > select up 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel red > save > /Users/visvaldas/Documents/work/quinone_reductase/green_red_3nitro_fig.cxs ——— End of log from Tue Feb 8 17:22:02 2022 ——— opened ChimeraX session > select clear > hide #3 models > hide #9 models > hide #8 models > hide #7 models > hide #6 models > show #6 models > hide #10 models > hide #11 models > select #1/A:127 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #1/A:126 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > show #7 models > save > /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs ——— End of log from Tue Feb 8 18:19:29 2022 ——— opened ChimeraX session > hide #6 models > hide #4 models > select #5/?:1@O3 1 atom, 1 residue, 1 model selected > select add #1/A:127@OG1 2 atoms, 2 residues, 2 models selected > ui tool show Distances > distance style symbol false > distance #5/?:1@O3 #1/A:127@OG1 Distance between 3nitroPNPDO_ox_docked_1.pdb #5/? UNK 1 O3 and 1qrd2_ref.pdb #1/A THR 127 OG1: 2.621 > hide #12.1 models > distance style color #aa7942 > distance style color black [Repeated 2 time(s)] > distance style color #010101 > distance style color #040404 > distance style color #0a0a0a > distance style color #101010 > distance style color #202020 > distance style color #282828 > distance style color #313131 > distance style color #434343 > distance style color #4e4e4e > distance style color #5b5b5b > distance style color #676767 > distance style color #7b7b7b > distance style color #858585 > distance style color #8d8d8d > distance style color #949494 > distance style color #a0a0a0 > distance style color #a4a4a4 > distance style color #a8a8a8 > distance style color #aeaeae > distance style color #b1b1b1 > distance style color #b4b4b4 > distance style color #b9b9b9 > distance style color #bbbbbb > distance style color #bdbdbd > distance style color silver > distance style color #c3c3c3 [Repeated 4 time(s)] > distance style color #c2c2c2 [Repeated 3 time(s)] > distance style color #c1c1c1 [Repeated 1 time(s)] > distance style color #bfbfbf [Repeated 1 time(s)] > distance style color #bebebe [Repeated 1 time(s)] > distance style color #bdbdbd > distance style color #b8b8b8 > distance style color #b5b5b5 > distance style color #b1b1b1 > distance style color #aaaaaa > distance style color #a6a6a6 > distance style color #a3a3a3 > distance style color #a0a0a0 > distance style color #9e9e9e > distance style color #9c9c9c > distance style color #9b9b9b > distance style color #9a9a9a > distance style color #989898 > distance style color #969696 > distance style color #949494 > distance style color #939393 > distance style color #919191 [Repeated 1 time(s)] > distance style color #909090 [Repeated 1 time(s)] > distance style color #8f8f8f [Repeated 2 time(s)] > distance style color #8e8e8e [Repeated 2 time(s)] > distance style color #8d8d8d [Repeated 1 time(s)] > distance style color #8c8c8c > distance style color #8a8a8a > distance style color #898989 [Repeated 1 time(s)] > distance style color #888888 [Repeated 1 time(s)] > distance style color #878787 > distance style color #858585 [Repeated 1 time(s)] > distance style color #848484 [Repeated 2 time(s)] > distance style color #838383 [Repeated 3 time(s)] > distance style color #828282 > distance style color #818181 > distance style color grey [Repeated 1 time(s)] > save > /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs > select clear > hide #7 models > select #5/?:1@N1 1 atom, 1 residue, 1 model selected > select add #1/A:126@OH 2 atoms, 2 residues, 2 models selected > distance #5/?:1@N1 #1/A:126@OH Distance between 3nitroPNPDO_ox_docked_1.pdb #5/? UNK 1 N1 and 1qrd2_ref.pdb #1/A TYR 126 OH: 3.115 > select clear > log metadata #1-11 No models had metadata > log chains #1-11 Chain information for 1qrd2_ref.pdb #1 --- Chain | Description A B | No description available Chain information for FADOx_receptor.pdb #2 --- Chain | Description A B | No description available Chain information for FADOx_receptor.pdb #3 --- Chain | Description A B | No description available > distance style color grey > select #5/?:1@N3 1 atom, 1 residue, 1 model selected > select add #1/A:126@OH 2 atoms, 2 residues, 2 models selected > distance #5/?:1@N3 #1/A:126@OH Distance between 3nitroPNPDO_ox_docked_1.pdb #5/? UNK 1 N3 and 1qrd2_ref.pdb #1/A TYR 126 OH: 2.903 > distance style color grey > save > /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs [Repeated 1 time(s)] ——— End of log from Tue Feb 8 22:40:34 2022 ——— opened ChimeraX session > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > select clear > ui tool show ""Side View"" > save > /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs No visible atoms, bonds, or surfaces selected > color #12 #fffb00 models transparency 0 > select clear > show #7 models > hide #7 models > save > /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs ——— End of log from Wed Feb 9 05:54:01 2022 ——— opened ChimeraX session > save > /Users/visvaldas/Documents/work/quinone_reductase/green_red_3nitro_fig.cxs > save > /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs > select :105 84 atoms, 90 bonds, 6 residues, 3 models selected > hide sel & #1-2 atoms > select clear > select :1-104 5156 atoms, 5282 bonds, 632 residues, 11 models selected > select :3-104 4920 atoms, 5022 bonds, 612 residues, 3 models selected > hide sel & #1-2 atoms > select :127-300 7174 atoms, 7369 bonds, 885 residues, 3 models selected > select :129-300 7060 atoms, 7249 bonds, 873 residues, 3 models selected > hide sel & #1-2 atoms > undo > select :129-250 5844 atoms, 5994 bonds, 732 residues, 3 models selected > hide sel & #1-2 atoms > select :106 66 atoms, 66 bonds, 6 residues, 3 models selected > hide sel & #1-2 atoms > select clear > save > /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs > lighting full > lighting simple > lighting soft > lighting full > lighting simple > save > /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs > save /Users/visvaldas/Documents/work/quinone_reductase/test.cxs > show #3 models > hide #3 models > show #3 models > hide #3 models > lighting full > lighting soft > lighting simple > hide #2 models > show #2 models OpenGL version: 4.1 INTEL-18.4.6 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,3 Processor Name: Quad-Core Intel Core i5 Processor Speed: 1.4 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 1715.81.2.0.0 (iBridge: 19.16.10744.0.0,0) OS Loader Version: 540.80.2~11 Software: System Software Overview: System Version: macOS 12.2 (21D49) Kernel Version: Darwin 21.3.0 Time since boot: 13 days 8:15 Graphics/Displays: Intel Iris Plus Graphics 645: Chipset Model: Intel Iris Plus Graphics 645 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea6 Revision ID: 0x0001 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 File attachment: test.cxs }}} [attachment:""test.cxs""] " defect closed normal Graphics limitation all ChimeraX