Thank you for the replies everyone.
I ended up removing NCS in refmac, and that seems to have corrected
the problem. Now the inserted residues (100A, 100B, etc) seem to have
refined properly, so I guess it was an NCS issue trying to put all the
similarily labelled residues to the same spot.
Anyways, I want to have NCS refinement, so I'll try putting the LINK
info in the header and try NCS again.
-----Original Message-----
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of John
Pak
Sent: Thursday, April 05, 2007 7:40 AM
To: [email protected]
Subject: [ccp4bb] antibody refinement in REFMAC with Kabat numbering
Hi all.
I'm currently refining an Fab structure. All was going reasonably well
until I renumbered the PDB according to the Kabat numbering convention.
After which, REFMAC does not refine the inserted residues properly (ie.
residues 82A, 82B, 100A, 100B, 100C, etc.). It refines these residues into
a steric jumble. I think REFMAC can't recognize that the residues are
connected or something.
So my question is, how do you refine this type of PDB in REFMAC? Or do you
just wait until the refinement is done, then change all the residue numbers
and connect entries in the header afterwards?
