[Chimera-users] Disulfide bonds

Elaine Meng meng at cgl.ucsf.edu
Wed Dec 5 09:05:10 PST 2012

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:

I hope this helps,
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

More information about the Chimera-users mailing list