On Thu, 2011-06-23 at 16:49 +0900, Masaki UNNO wrote:
> Dear all
> Is it possible to put restraint on only peptide bonds? I would like
> to put restraint on O-N bond lengths, Ca-O-N angles, and O=O-N angles.
> Could you teach me how to do it, if possible?
> Masaki UNNO, Ph.D.
One could create a monomer library with a set of alternative amino acids
(you'd rename them in the PDB-file too). Then, modeling a library after
the standard one, you assign alternative atom types and have a limited
set of defined bonds/angles. This would be quite painful to do though.
I wonder what will happen if you run unrestrained refinement yet provide
external distance restraints as described in refmac manual? Will the
external restraints be ignored? If not, then I'd think this is a better
approach. If yes, then maybe you can do the trick by using very high
weight matrix parameter (approaching the unrestrained refinement) and
correspondingly high external weight scale value.
Cheers,
Ed.
--
"Hurry up before we all come back to our senses!"
Julian, King of Lemurs
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