[Chimera-users] Questions about cartoon visualisation

[Elaine Meng]

Hello,
(1) yes, it is very simple, for example commands:

color gray,r coil
color red,r strand
color blue,r helix

...the ",r" part means ribbons only (not sticks, surface, etc.), see the color command help for details:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html>

See also command-line specifiers including coil, strand, helix:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#builtin>

(2) not exactly, you have to use the Ribbon Style Editor tool (in menu under Tools... Depiction) first to create the style that you want and give it a name. But after you save/name the style it is saved in your preferences and you can use "ribscale" or "ribrepr" to apply it, if it is a scaling (width/height) or style (cross-section shape) respectively.  This is all described in the Ribbon Style Editor help and links therein:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html>

If you want to do everything in the command line including specifying the angstrom values of width/height/etc. then you would need to use ChimeraX instead of Chimera.  In ChimeraX there is a "cartoon style" (same as "ribbon style") command that does all that stuff. See here for ChimeraX help for that command and several examples.
<https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On Feb 14, 2023, at 7:55 AM, Enrico Martinez via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear Chimera Users!
> 
> I have several basic commands related to the visualization of cartoon models:
> 
> 1) Is it possible to color secondary structure elements (normally integrated in the context menu by means of tools -> depiction) via some command called from command line / script ?
> 
> 2) how could I change the representation style of the cartoon diagrams e.g. radius of loops or introducing some artistic elements in alpha-helixes / B-sheets ? Is it possible to modify it via commands ?
> 
> Many thanks in advance
> 
> Best wishes
> 
> Enrico