id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4978 How to show backbone atoms with ribbon casey.vieni@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description I am trying to show a single sphere at c-alpha carbons for some point mutants that i designed. When I use the command: show /a:473,476,477 atoms I can see all the atoms in chain A for residues 473, 476, 477. Using: show /a:473,476,477@cb atoms I can show ""two spheres"" for the c-alpha and c-beta carbon. When I use: show /a:473,476,477@ca atoms nothing happens and i don't see any spheres. If I show the full atom and then do: hide /a:473,476,477@ca* atoms Just the c-alpha sphere gets hidden. Why is it that i can't just show the c-alpha spheres? Unfortunately for my figure i make silhouettes of my model and so i can't just hide the other atoms by making them fully transparent Log: UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > close > open > /Users/crv250/Documents/PhD_BhabhaEkiert/LetB/LetB_EM/LetB_models/6v0d_model2.pdb 6v0d_model2.pdb title: Lipophilic envelope-spanning tunnel B (letb), model 2 [more info...] Chain information for 6v0d_model2.pdb #1 --- Chain | Description A B C D E F | intermembrane transport protein yebt > view orient > view initial > set bgColor white > lighting soft > windowsize 300 800 > transparency /a,b,c,d,e,f 0 atoms > hide atoms > style sphere Changed 37920 atom styles > show /a cartoons > color /a,b,c,d,e,f:1-900 #969696 cartoons > view orient > turn x -90 > move z -100 > move y 80 > turn y -220 > turn x 10 > move z 50 > move y -4 > show /a cartoons > color /a:123,125,126 #B436EF cartoons > color /a:243,246,247 #5A42ED cartoons > color /a:355,358,359 #39C8F5 cartoons > color /a:473,476,477 #21FF52 cartoons > color /a:595,598,599 #DBFF00 cartoons > color /a:711,714,715 #FF7A00 cartoons > color /a:830,833,834 #FF0000 cartoons > color /a:830,833,834@CA #969696 cartoons > show /a:830,833,834 atoms > color /a:830,833,834@CA #969696 atoms > hide /a:830,833,834@cb atoms > show /a:595,598,599@cb atoms > show /a:711,714,715 atoms > hide /a:711,714,715@ca atoms > show /a:711,714,715@ca atoms > hide /a:711,714,715@cb atoms > hide /a:711,714,715@cg atoms > hide /a:711,714,715@cd atoms > hide /a:711,714,715@cg* atoms > hide /a:711,714,715@ca-cb atoms Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide /a:711,714,715@ca:cb atoms > show /a:711,714,715@ca:cb atoms > show /a:711,714,715@ca atoms > show /a:711,714,715@cb atoms > show /a:711,714,715@cd atoms > hide /a:711,714,715@cd atoms > hide /a:711,714,715@cg atoms > hide /a:711,714,715@cb atoms > hide /a:711,714,715@ca atoms > hide /a:711,714,715@cd* atoms > hide /a:711,714,715@cb* atoms > show /a:711,714,715@cb* atoms > show /a:711,714,715@ca* atoms > close > open > /Users/crv250/Documents/PhD_BhabhaEkiert/LetB/LetB_EM/LetB_models/6v0d_model2.pdb 6v0d_model2.pdb title: Lipophilic envelope-spanning tunnel B (letb), model 2 [more info...] Chain information for 6v0d_model2.pdb #1 --- Chain | Description A B C D E F | intermembrane transport protein yebt > view orient > view initial > set bgColor white > lighting soft > windowsize 300 800 > transparency /a,b,c,d,e,f 0 atoms > hide atoms > style sphere Changed 37920 atom styles > show /a cartoons > color /a,b,c,d,e,f:1-900 #969696 cartoons > view orient > turn x -90 > move z -100 > move y 80 > turn y -220 > turn x 10 > move z 50 > move y -4 > show /a cartoons > color /a:123,125,126 #B436EF cartoons > color /a:243,246,247 #5A42ED cartoons > color /a:355,358,359 #39C8F5 cartoons > color /a:473,476,477 #21FF52 cartoons > color /a:595,598,599 #DBFF00 cartoons > color /a:711,714,715 #FF7A00 cartoons > color /a:830,833,834 #FF0000 cartoons > show /a:123,125,126 atoms > show /a:243,246,247 atoms > show /a:355,358,359 atoms > show /a:473,476,477 atoms > show /a:595,598,599 atoms > show /a:711,714,715 atoms > show /a:830,833,834 atoms > hide /a:123,125,126@cb* atoms > hide /a:243,246,247@cb* atoms > hide /a:355,358,359@cb* atoms > hide /a:473,476,477@cb* atoms > hide /a:595,598,599@cb* atoms > hide /a:711,714,715@cb* atoms > hide /a:830,833,834@cb* atoms > hide /a:123,125,126@cd* atoms > hide /a:243,246,247@cd* atoms > hide /a:355,358,359@cd* atoms > hide /a:473,476,477@cd* atoms > hide /a:595,598,599@cd* atoms > hide /a:711,714,715@cd* atoms > hide /a:830,833,834@cd* atoms > hide /a:830,833,834@cg* atoms > hide /a:830,833,834@cb* atoms > hide /a:830,833,834@ce* atoms > show /a:830,833,834@ca* atoms > close > open > /Users/crv250/Documents/PhD_BhabhaEkiert/LetB/LetB_EM/LetB_models/6v0d_model2.pdb 6v0d_model2.pdb title: Lipophilic envelope-spanning tunnel B (letb), model 2 [more info...] Chain information for 6v0d_model2.pdb #1 --- Chain | Description A B C D E F | intermembrane transport protein yebt > view orient > view initial > set bgColor white > lighting soft > windowsize 300 800 > transparency /a,b,c,d,e,f 0 atoms > hide atoms > style sphere Changed 37920 atom styles > show /a cartoons > color /a,b,c,d,e,f:1-900 #969696 cartoons > view orient > turn x -90 > move z -100 > move y 80 > turn y -220 > turn x 10 > move z 50 > move y -4 > show /a cartoons > color /a:123,125,126 #B436EF cartoons > color /a:243,246,247 #5A42ED cartoons > color /a:355,358,359 #39C8F5 cartoons > color /a:473,476,477 #21FF52 cartoons > color /a:595,598,599 #DBFF00 cartoons > color /a:711,714,715 #FF7A00 cartoons > color /a:830,833,834 #FF0000 cartoons > show /a:123,125,126@ca* atoms > show /a:243,246,247@ca* atoms > show /a:355,358,359@ca* atoms > show /a:473,476,477@ca* atoms > show /a:595,598,599@ca* atoms > show /a:711,714,715@ca* atoms > show /a:830,833,834@ca* atoms > hide /a:123,125,126@cd* atoms > hide /a:243,246,247@cd* atoms > hide /a:355,358,359@cd* atoms > hide /a:473,476,477@cd* atoms > hide /a:595,598,599@cd* atoms > hide /a:711,714,715@cd* atoms > hide /a:830,833,834@cd* atoms > color /a:123,125,126 #B436EF atoms > color /a:243,246,247 #5A42ED atoms > color /a:355,358,359 #39C8F5 atoms > color /a:473,476,477 #21FF52 atoms > color /a:595,598,599 #DBFF00 atoms > color /a:711,714,715 #FF7A00 atoms > color /a:830,833,834 #FF0000 atoms > show /a:123,125,126@cb* atoms > show /a:243,246,247@cb* atoms > show /a:355,358,359@cb* atoms > show /a:473,476,477@cb* atoms > show /a:595,598,599@cb* atoms > show /a:711,714,715@cb* atoms > show /a:830,833,834@cb* atoms > hide /a:123,125,126@cb atoms > hide /a:243,246,247@cb atoms > hide /a:355,358,359@cb atoms > hide /a:473,476,477@cb atoms > hide /a:595,598,599@cb atoms > hide /a:711,714,715@cb atoms > hide /a:830,833,834@cb atoms > show /a:123,125,126@cb* atoms > show /a:243,246,247@cb* atoms > show /a:355,358,359@cb* atoms > show /a:473,476,477@cb* atoms > show /a:595,598,599@cb* atoms > show /a:711,714,715@cb* atoms > show /a:830,833,834@cb* atoms > hide /a:123,125,126@cb atoms > hide /a:243,246,247@cb atoms > hide /a:355,358,359@cb atoms > hide /a:473,476,477@cb atoms > hide /a:595,598,599@cb atoms > hide /a:711,714,715@cb atoms > hide /a:830,833,834@cb atoms > show /a:595,598,599@c[a] atoms > show /a:595,598,599@c[a]* atoms > show /a:595,598,599@c[a*] atoms > show /a:595,598,599@c[b] atoms > show /a:595,598,599@c[ab] atoms > hide /a:595,598,599@c[b] atoms > show /a:595,598,599@c[b] atoms > show /a:595,598,599 atoms > show /a:595,598,599@ca atoms > hide /a:595,598,599 atoms > show /a:595,598,599@ca atoms > show /a:595,598,599@cb atoms > hide /a:595,598,599 atoms > show /a:595,598,599 atoms > hide /a:595,598,599@ca atoms > show /a:595,598,599@ca atoms > hide /a:595,598,599@ca atoms > hide /a:595,598,599 atoms > show /a:595,598,599@ca atoms > show /a:595,598,599 atoms > select /a:595,598,599@ca atoms Expected a keyword > select /a:595,598,599@ca atoms Expected a keyword > hide /a:595,598,599@ca atoms > hide /a:595,598,599 atoms > show /a:595,598,599@ca > show /a:595@ca atoms > show /a@ca atoms > show /a:595,598,599@ca > show /a:595,598,599@ atoms > show /a:595,598,599 atoms > transparency /a:595,598,599@cg* 100 atoms > transparency /a:595,598,599@cd* 100 atoms > transparency /a:595,598,599@cb* 100 atoms > show /a:473,476,477 atoms > show /a:473,476,477 atoms > hide /a:473,476,477@cg* atoms > hide /a:473,476,477@cd* atoms > hide /a:473,476,477@cb* atoms > set silhouettes true > set silhouetteWidth 1 > set silhouetteColor black > show /a:473,476,477 atoms > hide /a:473,476,477@ca* atoms OpenGL version: 4.1 INTEL-16.1.10 OpenGL renderer: Intel(R) UHD Graphics 617 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir8,2 Processor Name: Dual-Core Intel Core i5 Processor Speed: 1.6 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1554.80.3.0.0 (iBridge: 18.16.14346.0.0,0) Software: System Software Overview: System Version: macOS 11.2 (20D64) Kernel Version: Darwin 20.3.0 Time since boot: 3:24 Graphics/Displays: Intel UHD Graphics 617: Chipset Model: Intel UHD Graphics 617 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x87c0 Revision ID: 0x0002 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: No 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: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-Clipper: 0.16.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 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: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.2.2 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 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: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 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: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 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: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.9 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.1 matplotlib: 3.3.2 matplotlib-inline: 0.1.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 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 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 }}} " defect closed normal Depiction not a bug all ChimeraX