Re: [ccp4bb] Atom labels in PDB file for Refmac

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

Previous message:
Subject: Atom labels in PDB file for Refmac
From: Anita Lewit-Bentley alewit {- at -} PASTEUR {- dot -} FR
Date: 2008-10-14

Next message:
Subject: Re: Atom labels in PDB file for Refmac
From: "Frances C {- dot -} Bernstein" fcb {- at -} BERNSTEIN-PLUS-SONS {- dot -} COM
Date: 2008-10-14

Subject: Re: Atom labels in PDB file for Refmac
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2008-10-14

Hi,

- MET residues should become MSE (i.e. Se-MET instead of S-Met)

- ' SD ' atom name should become 'SE '

- remove the columns 77-80

- run PDBSET to let it re-generate columns 77-80 again.

So something simple minded like

% grep "^CRYST1" your.pdb > tmp.pdb

% egrep "^ATOM
^HETATM" your.pdb

sed "s/ MET / MSE /g"

sed "s/ SD MSE/ SE MSE/g"

cut -c-76 >> tmp.pdb

% echo END
pdbset xyzin new.pdb xyzout new.pdb

should probably work. Ther might be something easier somewhere else,
maybe a really-fancy-function-with-a-meaningful-long-name-that-does-it
in Coot?

Cheers

Clemens

On Tue, Oct 14, 2008 at 05:24:34PM +0200, Anita Lewit-Bentley wrote:
> Dear all,
>
> This question may have been asked before, but I cannot find an answer in
> the recent ccp4bb archives - sorry!
>
> I am using an SeMet-protein data set as my native protein, since it
> diffracted to high resolution and should give all the information I need. I
> would therefore like to introduce the Se atom within the Met residue, so as
> to provide a correct description of the molecule.
>
> What format/syntax should I use for Refmac to recognise it? SED (with SE in
> he last column) does not work, nor does just simple SE left-shifted.
>
> Thanks for any hint!
>
> Anita
>
>
> Anita Lewit-Bentley
> Unité d'Immunologie Structurale
> CNRS URA 2185
> Département de Biologie Structurale & Chimie
> Institut Pasteur
> 25 rue du Dr. Roux
> 75724 Paris cedex 15
> FRANCE
>
> Tel: 33- (0)1 45 68 88 95
> FAX: 33-(0)1 40 61 30 74
> email: alewit@pasteur.fr
>

--

***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--------------------------------------------------------------
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CCP4bb navigation

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

Previous message:
Subject: Atom labels in PDB file for Refmac
From: Anita Lewit-Bentley alewit {- at -} PASTEUR {- dot -} FR
Date: 2008-10-14

Next message:
Subject: Re: Atom labels in PDB file for Refmac
From: "Frances C {- dot -} Bernstein" fcb {- at -} BERNSTEIN-PLUS-SONS {- dot -} COM
Date: 2008-10-14