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 > a.x.daw...@dundee.ac.uk -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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