Hi Dmitry,
I think the best way is not to make a new monomer. MAN-SER and MAN-THR
linkages do exist in the ccp4 monomer lib. If you simply build a mannose
with its O1 removed and put the C1 ~1.4 Angstrom to the OG of the serine I
think refmac should be able to detect the linkage. When this happens, you
should see a "LINKR ........MAN-SER " line in the header of the resulting
PDB file. COOT may not show a bond line for linkr record, but the real space
refine should work fine.
If you need to refine the structure with phenix.refine then you need to make
an edit file to specify that the mannose C1 is linked to the ser OG by a
covalent bond.
Zhijie
-----Original Message-----
From: Dmitry Rodionov
Sent: Wednesday, November 20, 2013 1:49 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Dealnig with O-linked mannose
Good day!
I am refining what appears to be O-mannosylated protein structure.
In my hands Coot (0.7.1) does not form the SER-MAN bond automatically.
I made a SER-MAN.cif with jLigand, which takes care of the glycosidic bond.
However, now the peptide bonds are not made to this custom residue (same
chain, consecutive numbering).
Am I doing something wrong? How can I fix this?
Many thanks,
Dmitry
