Re: [ccp4bb] antibody refinement in REFMAC with Kabat numbering

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: Klaus_Fütterer k {- dot -} futterer {- at -} BHAM {- dot -} AC {- dot -} UK
Date: 2007-04-05

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Subject: Re: antibody refinement in REFMAC with Kabat numbering
From: John Pak john {- dot -} pak {- at -} UTORONTO {- dot -} CA
Date: 2007-04-05

Subject: Re: antibody refinement in REFMAC with Kabat numbering
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2007-04-05

A common lament on Kabat fabs.

You need to modify the LINK statement for this purpose
for the residues in question.

Read the REFMAC log and PDB and you will
see that it recognized the link but still did not use it.

The correct format for the link statement
needs the 'gap' in the pdb file refmac writes replaced with 'TRANS'

I squawked this a while ago.

BR

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] 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?

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
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From: Klaus_Fütterer k {- dot -} futterer {- at -} BHAM {- dot -} AC {- dot -} UK
Date: 2007-04-05

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Subject: Re: antibody refinement in REFMAC with Kabat numbering
From: John Pak john {- dot -} pak {- at -} UTORONTO {- dot -} CA
Date: 2007-04-05