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.
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
