On 22/11/11 00:16, Jan van Agthoven wrote:
Hi everyone!
Does anyone know if there is a way of auto-refining a sugar in Coot?
Such a tool (if I understand correctly what you want) does not yet
exist. However, I believe that things are not in as poor a state as one
might infer from other posts.
Using the pre-release, you can
1) ideally position a NAG onto ASN
2) use multi-residue torsion to position a NAG by rotation of ASN chi angles
3) use the Ligand builder to build new carbohydrate monomers (it is my
experience that PRODRG respects the wedge bonds - but I have heard that
this is not always the case)
Using latest stable or later you can
4) multi-residue refinement (or sphere refine), which does a link
analysis based on the coordinates of the residue selection (note that
bonding atoms have to be within 3A to be considered a real glycosidic
linkage)
5) add addition pseudo plane restraints to encourage ideal chair (in my
experience, at low resolution or with poor density, carbohydrates tend
to wander off and twist up without these)
The JLigand-Coot interface has stalled a bit, but I hope should be
available for the Study Weekend.
The Refmac-Coot link-up using LINKR is under discussion with Garib and
Eugene.
I would recommend against making a synthetic disaccharide carbohydrate
with PRODRG.
Regards,
Paul.
