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#4978 closed defect (not a bug)

How to show backbone atoms with ribbon

Reported by:	casey.vieni@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Depiction	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

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

Change History (2)

comment:1 by Tom Goddard, 4 years ago

Component:	Unassigned → Depiction
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → How to show backbone atoms with ribbon

I guess you are trying to show the CA atoms and the ribbon at the same time. The ribbon suppresses the display of backbone atoms. To allow displaying backbone atoms with the ribbon use the following as described in the documentation https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cartoon.html

cartoon #1 suppressBackbone false

To hide backbone atoms

hide /a & backbone

To show a few CA atoms

show /a:473,476,477@ca

To make those CA atoms sphere style so they are bigger

style /a:473,476,477@ca sphere

comment:2 by Tom Goddard, 4 years ago

Resolution:	→ not a bug
Status:	assigned → closed

Send questions about how to use ChimeraX to chimera-users@… rather than making a bug report. That way everyone will benefit from the answer. Thanks.

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