Questions about cartoon visualisation
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
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@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
Thank you very much, Elaine ! 😘 Yours sincerely Enrico Il giorno mar 14 feb 2023 alle ore 17:27 Elaine Meng <meng@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#built...
(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/ribbo...
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@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
participants (2)
-
Elaine Meng -
Enrico Martinez