The issue I would raise here is not just for coot, but also for PDB format itself. Last time I asked on ACA2011, Dr. Berman said polysacchride residues in PDB is still not yet uniformly represented.
The issue I have is to polysacchride chains refinement in general, but here more specific about branch chain of polysacchride chains. For example, if you think about the case of N-glycosylation Asn-NAG-beta1,4-NAG-beta1,4-Man-(alpha1,3-Man)-alpha1,6-Man ... Now you have a branch chain, Now if I assume the following resseq ASN A135 NAG A500 NAG A501 MAN A502 MAN A503 MAN A504 In my coot, version 0.6 revision 2540, You will be able to refine A500-A503 as a whole since they are consecutive in resseq. But when I need to refine NAG A500 together with ASN A135 locally, simply specify the range is not enough, I need to specify a small radius to get it work, even though the covalent link is defined in LINKR record. The same applies when I want to refine just A502-A504 alpha1,6 glycosidic bond without refine A503. I am just wondering what is the state of the art for branch chain handling in coot or another interactive refinement program. best regards, Heping Zheng > 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. >
