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 >
