Hi Folmer, RAF is in the PDB ligand dictionary with status 'REL' so you can use it. If RAF is a subset of something bigger, then perhaps you should use monosaccharide building blocks. If in doubt, ask a PDB annotator. Anyway, PDB-care will check whether the connectivity in a compound named RAF matches the standard description of RAF. CARP will check the torsion angles between the monosaccharide building blocks.
HTH, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Folmer Fredslund > Sent: Thursday, February 21, 2013 15:37 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Building sugars > > 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 <robbie_joos...@hotmail.com> > > > 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:CCP4BB@JISCMAIL.AC.UK] On > > Behalf Of Folmer Fredslund > > Sent: Thursday, February 21, 2013 12:33 PM > > To: CCP4BB@JISCMAIL.AC.UK > > 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
