[Chimera-users] Batch mode for Chimera

James Starlight jmsstarlight at gmail.com
Fri Sep 8 03:07:32 PDT 2017


P.S. That option was the source of the problem - #set silhouette

2017-09-08 10:22 GMT+02:00 James Starlight <jmsstarlight at gmail.com>:
> 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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