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Re: [ccp4bb] antibody refinement in REFMAC with Kabat numbering
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: oxidised cys
From: stefano ricagno ciciulus {- at -} HOTMAIL {- dot -} COM
Date: 2007-04-10		Next message:
Subject: Re: Summary - Valid to stop Refmac after TLS refinement?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-04-10


Subject: Re: antibody refinement in REFMAC with Kabat numbering
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-04-10

John Pak wrote:
> 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?
>
>
Yes! - or better, let the deposition site renumber if they must.. I feel
these weird numbering schemes are archaic - we can easily align
sequences and see that 82A is actually 83 etc.. But that is a personal view.

Eleanor

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: oxidised cys
From: stefano ricagno ciciulus {- at -} HOTMAIL {- dot -} COM
Date: 2007-04-10		Next message:
Subject: Re: Summary - Valid to stop Refmac after TLS refinement?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-04-10
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