id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14746 "How ""name"" works" olibclarke@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.3.1-arm64-arm-64bit ChimeraX Version: 1.8.dev202403091657 (2024-03-09 16:57:27 UTC) Description More of a feature request than a bug: Name does not work with ""sel"" as spec. Namesel in Chimera was useful to save a complicated and sometimes graphically selected set of atoms for later reference (""namesel my_selection sel""). ""Name"" in ChimeraX serves a similar function, but only seems to take an explicit atom-spec - if I try a name command with ""sel"" as the spec, it does not return anything later. It would be convenient if it did. Cheers Oli Log: > runscript /Users/oc2188/Dropbox/chimera_startup/chimerax_startup.py > camera ortho > cofr centerOfView > mousemode alt rightMode ""contour level"" > mousemode rightMode clip > mousemode alt leftMode ""translate selected models"" > mousemode shift leftMode ""rotate selected models"" > mousemode alt control leftMode ""pick blobs"" > alias cofron cofr centerofview showpivot 7,0.25 > alias cofroff cofr centerofview showpivot false > alias symclip cofr centerofview; clip near -$1 far $1 position cofr > alias cootmode set bgColor black; surface cap false; surface style solid; > lighting flat; graphics silhouettes false; style stick; ~rib; color > ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style > solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70; > cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues > cornflower blue > alias cootmode_mesh surface cap false; surface style mesh; lighting flat; > graphics silhouettes false; style stick; ~rib; color ##num_residues gold; > color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size > ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far > 10 position cofr; color ##~num_residues #3d60ffff; transparency 50 > alias project_map set bgColor black; lighting depthcue false; volume $1 > style image sdlevel 0,0 color white sdlevel 100,0.15 color white > projectionmode 3d maximumIntensityProjection false dimTransparentVoxels > false btcorrection true showOutlineBox false linearinterpolation true > alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; > disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp > ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1 > alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp > @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius > 0.1 > alias map_sphere_15 volume unzone ##~num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; volume zone ##~num_residues nearAtoms sel > minimalBounds true range 15; close #10000 > alias map_unsphere volume unzone ##~num_residues > alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5; > lighting soft > alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel > distance 0; close #10000 > alias showmaps surface unzone ##~num_residues > alias caps_off surface cap false > alias caps_on surface cap true > alias open_vseries ""open browse vseries true"" > alias selbetween ks ri > alias helix setattr $1 res is_helix true > alias strand setattr $1 res is_strand true > alias coil setattr $1 res is_strand false; setattr $1 res is_helix false > alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136; > movie encode ~/Desktop/rock_movie.mp4; stop > buttonpanel Shortcuts rows 3 columns 5 > buttonpanel Shortcuts add Vol_Viewer command ""tool show 'Volume Viewer'"" > buttonpanel Shortcuts add Model_Panel command ""tool show Models"" > buttonpanel Shortcuts add Log command ""tool show Log"" > buttonpanel Shortcuts add default_disp command default_mol_display > buttonpanel Shortcuts add map_sphere command map_sphere_15 > buttonpanel Shortcuts add map_unsphere command map_unsphere > buttonpanel Shortcuts add cofron command cofron > buttonpanel Shortcuts add cofroff command cofroff > buttonpanel Shortcuts add cootmode command cootmode > buttonpanel Shortcuts add mark_cofr command ""marker #20000 position cofr"" > buttonpanel Shortcuts add hidemaps command hidemaps > buttonpanel Shortcuts add showmaps command showmaps > buttonpanel Shortcuts add reset_mouse command ""mousemode alt right contour ; > mousemode right clip ; mousemode alt left 'translate selected models' ; > mousemode shift left 'rotate selected models' ; mousemode alt control left > 'pick blobs'; help https://github.com/olibclarke/chimerax- > trimmings/blob/main/default_mousemodes.md"" > buttonpanel Shortcuts add previous_model command prevmodel > buttonpanel Shortcuts add next_model command nextmodel > volume defaultvalues limitVoxelCount false voxelLimitForPlane > 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true Saved volume settings UCSF ChimeraX version: 1.8.dev202403091657 (2024-03-09) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1bl8 format mmcif fromDatabase pdb 1bl8 title: Potassium channel (KCSA) from streptomyces lividans [more info...] Chain information for 1bl8 #1 --- Chain | Description | UniProt A B C D | PROTEIN (POTASSIUM CHANNEL PROTEIN) | KCSA_STRLI 23-119 Non-standard residues in 1bl8 #1 --- K — potassium ion > marker #20000 position cofr > ui mousemode right ""translate selected models"" > select #20000/M:1@M 1 atom, 1 residue, 1 model selected > view matrix models #20000,1,0,0,0.76997,0,1,0,0.96001,0,0,1,-0.7072 > ui tool show ""Side View"" > select clear [Repeated 1 time(s)] > select #20000/M:1@M 1 atom, 1 residue, 1 model selected > select clear > select #20000/M:1@M 1 atom, 1 residue, 1 model selected > view matrix models #20000,1,0,0,2.6376,0,1,0,-0.52886,0,0,1,-1.9265 > view matrix models #20000,1,0,0,3.207,0,1,0,-1.0436,0,0,1,-2.433 > help mousemode > view matrix models #20000,1,0,0,3.3695,0,1,0,-1.0304,0,0,1,-0.48329 Drag select of 1 atoms > select #20000/M:1@M 1 atom, 1 residue, 1 model selected Drag select of 1 atoms > view matrix models #20000,1,0,0,3.7692,0,1,0,-0.8104,0,0,1,-1.2713 > view matrix models #20000,1,0,0,5.3784,0,1,0,-2.3995,0,0,1,-0.26464 > help turn > select clear > turn y 90 [Repeated 3 time(s)] > select #1/A:403@K 1 atom, 1 residue, 1 model selected > select add #1/A:401@K 2 atoms, 2 residues, 1 model selected > turn sel 90 [Repeated 2 time(s)] > cofron > select clear > select #1/D:104 4 atoms, 3 bonds, 1 residue, 1 model selected > select clear > select #1/A:401@K 1 atom, 1 residue, 1 model selected > select add #1/A:403@K 2 atoms, 2 residues, 1 model selected > namesel custom axis Unknown command: namesel custom axis > help namesel No help found for 'namesel' > select up 708 atoms, 724 bonds, 100 residues, 1 model selected > select up 2824 atoms, 2896 bonds, 392 residues, 1 model selected > select down 708 atoms, 724 bonds, 100 residues, 1 model selected > select down 2 atoms, 2 residues, 1 model selected > name sel custom_axis ""sel"" is reserved and cannot be redefined > name custom_axis sel > select clear > turn custom_axis 90 Expected an axis vector or a keyword > turn custom_axis 90 Expected an axis vector or a keyword > turn custom_axis 90 Expected an axis vector or a keyword > turn custom_axis 90 Expected an axis vector or a keyword > turn 90 custom_axis Expected an axis vector or a keyword > turn 90 custom_axis Expected an axis vector or a keyword > turn 90 custom_axis Expected an axis vector or a keyword > turn 90 custom_axis Expected an axis vector or a keyword > turn 90 custom_axis Expected an axis vector or a keyword > select custom_axis Nothing selected > help name > select custom_axis Nothing selected > custom_axis Unknown command: custom_axis > select #1/A:401@K 1 atom, 1 residue, 1 model selected > select add #1/A:403@K 2 atoms, 2 residues, 1 model selected > name custom_axis sel > name list custom_axis sel > tool show Log > name custom_axis custom_axis sel > select clear > select custom_axis Nothing selected > help name > select #1/A:403@K 1 atom, 1 residue, 1 model selected > select add #1/A:401@K 2 atoms, 2 residues, 1 model selected > name custom_axis sel > name custom_axis @K* > select custom_axis 3 atoms, 1 pseudobond, 3 residues, 2 models selected OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M2 Max OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,5 Model Number: Z17J00171LL/A Chip: Apple M2 Max Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 64 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: 11 days, 23 hours, 47 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 30 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: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.14.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.1.1 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.16 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.3 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.5 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.54.6 ChimeraX-AtomicLibrary: 14.0.2 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: 2.12.1 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: 1.4 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.dev202403091657 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: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.9 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.2 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-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.3 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.1 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-Segmentations: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.2 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.36.1 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 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.8 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.1 fonttools: 4.49.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 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: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 Jinja2: 3.1.3 jupyter-client: 8.6.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.1.0 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.2 matplotlib-inline: 0.1.6 msgpack: 1.0.8 ndindex: 1.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.2.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.9.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.3 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.2.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.0 prompt-toolkit: 3.0.43 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.3.0 pygments: 2.17.2 pynmrstar: 3.3.3 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3302 pyparsing: 3.1.2 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.2 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.2 python-dateutil: 2.8.2 pytz: 2024.1 pyzmq: 25.1.2 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.12.0 setuptools: 69.1.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.0 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.1 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.1 typing-extensions: 4.10.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.42.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect closed normal Command Line not a bug Elaine Meng all ChimeraX