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@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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