[Chimera-users] Batch mode for Chimera

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 6 09:34:51 PDT 2017


Hi Gleb,
Yes, but then you don’t know which one of those commands might show the graphics driver problem!  I guess you can experiment with which parts will work.  The descriptions of the presets say what they include:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/preset.html>

Then you can identify individual commands to do those things. Most of the stuff is in the “set” command, see
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html>

Publication preset 2 includes white background and silhouette edges, commands:

set bgcol white
set silhouette

It also turns off depth-cueing (mist):

~set depth

… and changes to “licorice” style ribbons (which doesn’t show helix and strand differently):

ribscale licorice

You might also be interested in other “set” options  (see link above), and “lighting”:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/lighting.html>

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

> On Sep 6, 2017, at 12:49 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> 
> Thank you, Elaine!
> 
> Regarding presets
> Is it possible to define step-by-step some commands to obtain
> something like preset 2 visualization state?
> 
> Gleb




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