[Chimera-users] Disulfide bonds

[Elaine Meng]

On Dec 5, 2012, at 1:20 AM, Moritz Bitzhenner wrote:

> Hi Elaine,
> You are a lifesaver. Thank you very much, it all worked perfectly. Now I have a nice colourful ribbon structure protein with disulfide bonds. The middle of the bond is coloured in yellow, the rest of the sidechain is coloured in light grey. Can I change the colour of the grey sidechain without changing the colour of the AA in the ribbon structure? But it´s not that important.
> 
> I also created a movie of the rotating protein. (Command line: roll). Can I decrease the speed of the rotation?
> 
> With best regards from Germany and many thanks for your help.
> Moritz

Hi Moritz,
Greetings to you in Germany!

You can specify that coloring should apply only to atoms/bonds (not ribbons, surfaces, etc.) using the Color Actions dialog.  Menu: Actions... Color... all options, and then in that dialog see the "Coloring applies to" section.

The same thing can be done in the command line, for example:

color goldenrod,a :cys

...means to make atoms-only of Cys residues the color named goldenrod.

Each command has a manual page, which you can see with the "help" command (e.g. commands "help roll" "help color") so I recommend looking at those for more details such as how to control the speed of roll.  See also the general information on making movies:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. best to send to chimera-users at cgl.ucsf.edu so that others can benefit