Dear Alice,
There is a very simple workaround: simply don't deposit the hydrogen
atoms (if you use the B option in SHELXPRO to prepare the deposition
this is the default anyway). SHELXL refined them as a riding model for
the xyz and B values anyway. If anyone needs them later they can easily
regenerate them, e.g. using MolProbity. This workaround also sidesteps
the RCSB cheking the chirality of the CH2-groups.
Best wishes, George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582
On Wed, 12 May 2010, 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]
>
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