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.

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