It looks like a bug. Insertion code should have been used in NCS
restraint definitions. It seems it does not. I will try to fix
it asap.
Insertions are usually no problem. Problems arise when you have
deletions (i.e. residue numbering is
not sequential). Then you need to use LINK record with TRANS name for
the link.
Garib
On 5 Apr 2007, at 18:43, John Pak wrote:
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: CCP4BB@JISCMAIL.AC.UK
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?
