[Chimera-users] Questions about cartoon visualisation

[Enrico Martinez]

Thank you very much, Elaine !  😘

Yours sincerely

Enrico

Il giorno mar 14 feb 2023 alle ore 17:27 Elaine Meng <meng at cgl.ucsf.edu> ha
scritto:

> 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
>
>
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