On 25/07/12 16:20, Sebastiano Pasqualato wrote:
Hi there,
I'd like to model a thioester bond, starting from protein A with an
exposed Cys, and having juxtaposed the carboxyl group of a C-terminal
residue of protein B.
The way I would like to proceed is by:
1) telling coot that there's a bond between the S atom and the C atom
of the two groups;
2) regularize that zone in order to have something that makes chemical
sense.
Could you advice me on how to proceed for the two steps?
That is, how do I tell coot that the bond exists and it has to be
taken into account?
You want to use the JLigand and the JLigand-Coot interface...
(which we will demonstrate on Saturday).
IIRC, JLigand is available in CCP4 6.3.0 or from York
http://www.ysbl.york.ac.uk/mxstat/JLigand/index.html
http://lmb.bioch.ox.ac.uk/coot/screenshots/coot-jligand-1.ogv
Paul.
