Dear Alice,
I don't know what the consensus about this is and I don't know your resolution.
But if you really only have hydrogens in riding positions and did not refine
them you might as well deposit the structure without hydrogens in the PDB-file.
You could also check if shelxpro deals with the problem differently than the
default output from shelxl, I did not try myself.
If your hydrogen atoms follow a particular pattern you might also be able to use
shell utilities like sed to rename the hydrogrens to a three-letter format.
Tim
On Wed, May 12, 2010 at 11:38:26AM +0100, Alice Dawson wrote:
> Usual apologies for non-CCP4 question.
>
> I have been working on two high resolution protein structures using
> Shelx for refinement.
>
> I included idealised riding C-H and mainchain amide N-H hydrogens in
> the refinement. In the PDB output by Shelxl the hydrogen atom names for
> valine, threonine, isoleucine and leucine are truncated from four
> characters (in the .res) to three. This results in duplicate names for
> atoms in these residues which is causing difficulties in depositing the
> structures. Each structure has over 1000 residues in the asymmetric unit
> so manually altering the names without introducing other errors is
> difficult. Does anyone know of any workaround?
>
> cheers
> Alice
>
>
> Alice Dawson
>
> Biological Chemistry and Drug Discovery
> College of Life Sciences
> The Welcome Trust Building
> University of Dundee
> Dow Street
> Dundee DD1 5EH
>
> Tel. 01382 385744
> [log in to unmask]
--
--
Tim Gruene
Institut fuer anorganische Chemie
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D-37077 Goettingen
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