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

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

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

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

Next message:
Subject: Re: antibody refinement in REFMAC with Kabat numbering
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-04-05

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

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: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?
>
>
>

CCP4bb navigation

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

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

Next message:
Subject: Re: antibody refinement in REFMAC with Kabat numbering
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-04-05