[Chimera-users] Visualising disulfide bonds

[Elaine Meng]

Hi George,
If the bonds were literally present in the trajectory (defined in the prmtop), they would be shown if you were showing Cys atoms and bonds, and you could select them using "Select... Chemistry... functional group... disulfide" or command: sel disulfide

However, if they are not explicitly defined as bonds and you simply want to identify when cysteine sidechains come close to each other, you would need to do distance measurements instead.  It wouldn't work to find cysteines within some zone of a cysteine since of course, each would be within the zone of itself, so you would need to either (a) use residue numbers and measure the SG-SG distance for each possible pair, or (b) use a python script that does the zone "except self."  Neither of these would check for reasonable angles for bonding, however.

For (b) there is a similar script "selLys.py" available on our wiki
<http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts>
You would need to change it from using lysine NZ and 8 angstroms to cysteine SG and whatever cutoff you feel appropriate.

The command or script could be used on your trajectory on a per-frame basis (see Per-Frame menu of MD Movie).
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>

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

On Nov 12, 2011, at 3:33 AM, George Tzotzos wrote:

> Hi everybody,
> I'm trying to find a way to visualise disulfide bonds in AMBER trajectory files to no avail.
> Any help how to do so will be very much appreciated.
> Regards
> George