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: [EMAIL PROTECTED]
>
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