[ccp4bb] antibody refinement in REFMAC with Kabat numbering

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CCP4bb <-- 2007 <-- April 2007 <-- 05 April 2007

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Subject: Re: Summary - Valid to stop Refmac after TLS refinement?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-04-05

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From: Jobichen Chacko jobichenc {- at -} NUS {- dot -} EDU {- dot -} SG
Date: 2007-04-05

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

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?

CCP4bb navigation

CCP4bb <-- 2007 <-- April 2007 <-- 05 April 2007

Previous message:
Subject: Re: Summary - Valid to stop Refmac after TLS refinement?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-04-05

Next message:
Subject: Summary: Multiple nucleation.
From: Jobichen Chacko jobichenc {- at -} NUS {- dot -} EDU {- dot -} SG
Date: 2007-04-05