Hi all Thank you all for your replies.
I might have expressed myself poorly, but I am not talking about covalently linked sugar modifications, so for my purpose there's no need to be concerned about insertion codes ;-) The glycosciences.de link is really useful. There does not seem to be a test to verify correct PDB nomenclature though. Or perhaps RAF (for raffinose, a tri-saccharide) is OK to use? Best regards, Folmer 2013/2/21 Robbie Joosten <[email protected]> > Hi Folmer, > > Just to add some tips: > > > Concerning the naming as one molecule: the sugar monomers get the same > > chain ID as the protein they are connected to and arbitrary residue > numbers. > > I usually start numbering from 1000 to prevent overlap with the numbering > > of the amino acids. > 1) Just don't use insertion codes, some people find it upsetting ;) And > keep > the residue numbering consistent between NCS copies. > > 2) The glycosciences.de portal has many tools for dealing with > carbohydrates: http://www.glycosciences.de/ > I really like PDB-care and CARP for validation in the building and > refinement process. > > 3) When using TLS you should try to figure out whether it's useful to add > the sugars to the group of the linked protein residue or to have specific > groups for your sugar trees. > > Cheers, > Robbie > > > HS. > > > > > > ________________________________ > > > > From: CCP4 bulletin board [mailto:[email protected]] On > > Behalf Of Folmer Fredslund > > Sent: Thursday, February 21, 2013 12:33 PM > > To: [email protected] > > Subject: [ccp4bb] Building sugars > > > > > > Dear all, > > > > > > > > What's the "correct" way to build and refine sugar polymers? > > > > > > I am currently building several structures with different kinds of > sugar > > polymers bound to them. > > > > > > Searching for similar "ligands" in the PDB, I end up with e.g. > > trisaccharides that are named as one molecule, even though they are > indeed > > made up of three individual sugars with bonds between them. > > > > > > > > Thank you for any pointers. > > > > > > Best regards, > > Folmer > > > > > > -- > > Folmer Fredslund > > > -- Folmer Fredslund
