It seem the LINK line I provided eariler was chopped by the email system.
Here it is again:
LINKR********C1**MAN*C***1*****************OG**SER*B*912****************MAN-SER
Simply replace each * with a space and change the residue IDs.
Also to clarify the procedure of using refmac to generate the MAN-SER
linkage line:
1 In COOT, get monomer->MAN, delete hydrogens, delete O1. Drag the MAN to
the proper position. C1 has better be ~1.4A away from OG and mind the
anomer conformation.
It seems that refmac detects covalent bonds mainly based on the distances.
If you accidentaly put the ligand too close to something it should not be
linked to (happens when you have poor electron density for positioning the
ligand), refmac might complain that a new ligands is found but the geometry
information is not provided. In such case the error message is a little
misleading to the user: it is a new covalent bond, not a new monoer that's
not described.
2 Merge molecules, Save PDB. For linkages that can be found in the standard
monomer lib, you do not need to make the bond in COOT. It is refmac that
will add this record.
3 Send the saved PDB to refmac. Do restrained refinement.
4 Check the resulting PDB to see if you now have the LINKR...MAN-SER line.
And in the refmac log you can find this line:
WARNING : link:MAN-SER is found dist = 1.178 ideal_dist= 1.439
ch:BB res: 912 SER at:OG .->CC res: 1 MAN
at:C1 .
Zhijie
-----Original Message-----
From: Dmitry Rodionov
Sent: Thursday, November 21, 2013 4:09 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Dealnig with O-linked mannose
Thank you all for helpful suggestions.
My question was how to properly connect a mannose to a serine and real-space
refine the result. My apologies for not being clear enough.
Coot can't find MAN-SER or SER-MAN in it's library (Coot 0.7.1, mon_lib
5.41)
It does not automatically make the bond between MAN C1 and OG of SER either.
Here is the way I finally made the connection followed by refinement it in
Coot:
1) Get monomer... MAN
2) real-space refine MAN into reasonable position
3) Delete hydrogens and reducing hydroxyl
Bond is not detected
4) Extensions->Modelling ...->make Link (Click 2 atoms) ... Click on C1 of
MAN and OG of SER
dashed bond appears
5) Sphere refine
A whole different issue that was touched in the replies is how this model
will be handled by refinement programs.
For the sake of a record, I am using Phenix and it seems to not respect the
described link without massaging by means of either pdb.edits or
apply_link.def.
Also, phenix.refine does not produce LINK records in the output PDB, so step
4 might have to be repeated.
Best regards,
Dmitry
