[Chimera-users] modifying presets

[Elaine Meng]

Hi Glenn,
Although we plan to have user-defined presets in the future,  
currently there is no reasonably user-friendly way to customize them.

As a stopgap, if there are a few commands that generate the display  
you want (and you could start with a preset command), you could:

- put them in a command file; simply opening the command file in  
Chimera would execute it

- alias some word like "mypreset1" to those commands all strung  
together with semicolons, then later you would only have to type the  
command "mypreset1"
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html

You can have a command file automatically read at Chimera startup.  
This is specified in the preferences:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Midas

You would only put the alias commands there, not the display commands  
themselves, since you want to control when those commands are  
executed (and usually at startup no structures have been opened yet  
anyway).

There is also a New Molecules section of the preferences in which you  
can control how structures are displayed when they are first opened:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New% 
20Molecules

However, the New Molecules options are rather limited compared to  
what you can do with commands.  There is nothing about disulfide  
bonds, for example.

I would be happy to provide more detailed help with any of this if  
you would like.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Feb 20, 2008, at 3:31 PM, glenn millhauser wrote:

> Hi Folks,
>    Is there a way to edit the Presets to include additional protein  
> features?  Specifically, I work with quite a few disulfide rich  
> proteins and it would be great to select the Preset Interactive 1  
> and have it automatically draw Cys side chains with disulfide links.
> Many thanks,
> glenn
>
>
> Glenn L. Millhauser
> Department of Chemistry & Biochemistry
> UC Santa Cruz
> Santa Cruz, CA 95064
> 831 459 2176 voice
> 831 566 3337 cell
> 831 459 2935 fax
>
> http://chemistry.ucsc.edu/~glennm
> http://www.chemistry.ucsc.edu/faculty/millhauser.html
>
>
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