[Chimera-users] Batch mode for Chimera

James Starlight jmsstarlight at gmail.com
Fri Sep 8 01:22:30 PDT 2017


Thank you so much, Elaine!

2017-09-06 18:34 GMT+02:00 Elaine Meng <meng at cgl.ucsf.edu>:
> 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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