Dear Hailiang
There are several protein-sugar and sugar-sugar link defined in the standard
refmac library.
You may try running refmac with the default options with the input pdb file in
which
- sugar residues included,
- no LINK record are specified.
If all required links are in the refmac's
Dear Hailiang,
While apparently no response came, here my 2 cents:
Even if there would be an automatic utitility to generate links based on
distances, I would never use it. Either the sugars have been properly
refined and then the link cards are present in the pdb file, or the
sugars have been
Dear Hailiang,
as Herman Schreuder already wrote sugars are quite likely to contain errors. We
are developing the PDB CArbohydrate REsidue check tool (pdb-care) in our group
to help crystallographers locating problems in sugars. There will be an update
soon, which includes checks for
Does anybody know the pdb codes with proteins with O-linked
sugars on THR.
I support a program to help interpret sugars in poor electron density
by stabilizing links. Coot helps a bit but branching poses a problem.
Rather than based on distance like coot operates at present it should be
best
Dear Enrico,
you can find information on PDB entries with carbohydrates in the
GLYCOSCIENCES.de database:
http://www.glycosciences.de/database/index.php
To find entries with O-Glycans linked to Thr you can use the substructure
search at
