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On Thu, 22 Apr 2010 10:13:40 -0700, tirumal <[log in to unmask]> wrote: > If you have a poor density (which I guess, generally is the case for large glycoprotein structures) you have to depend on trial and error strategy to get the right NAG conformation. I don't know how other refinement programs handle this, but after Phenix.refinement run, one has to definitely check the geometry of the NAGs carefully. I would like to add two further resources to the list of URLs already posted by Kim in this thread: You can use the PDB CArbohydrate REsidue check (pdb-care) tool to check carbohydrate residue geometry: http://www.glycosciences.de/tools/pdb-care/ This program detects carbohydrates, tries and assigns correct PDB residue names and checks, if they match the residue names used in the uploaded file. We will also add some further validation of N-glycan structures to notify users of "unusual" residues such as a-D-GlcpNAc (NDG) instead of b-D-GlcpNAc (NAG) in the N-glycan core structure. Kim already mentioned GlycoMapsDB to find the preferred conformations. The CARP (CArbohydrate Ramachandran Plot, http://www.glycosciences.de/tools/carp/) software helps you to check the conformation of glycosidic linkages by creating Ramachandran plot-like images. You can compare the glycosidic torsions in your structure either to computed maps from the GlycoMapsDB or to the glycosidic linkage conformations found in the PDB. > Hope to see a validation tool for NAGs in Coot soon. We are planning to implement some of the pdb-care checks in Coot, but of course this will take some time. Thomas