Dear Folmer,
I build them from monomers like NAG, MAN, FUC etc. It used to be quite
messy (reason why people put in triscaccharides??) but works fine
nowadays. You have to put in LINK records to specify the connections and
remove the oxygen which gets replaced by the link (usually O1). There
should be plenty of files like that in pdb (like 4az3, which I deposited
recently...).
Good luck!
Herman
________________________________
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
