[phenixbb] problem to add D atom on carbonyl group (enol) as alternate conformation

Ralf Grosse-Kunstleve rwgrosse-kunstleve at lbl.gov
Thu Oct 27 04:21:45 PDT 2011

Hi Maxime,
Could you send me (not the list) the three residues from your PDB file with
the tricky residue in the middle, including the D atom (roughly) where you
want it?

On Thu, Oct 27, 2011 at 2:58 AM, Maxime Cuypers <cuypers at ill.fr> wrote:

> Dear all,
> i have a problem that i block on for quite a while. i need to add a D atom
> on carbonyl group (enol) as alternate conformation to a main chain protein
> amide group to refine with phenix.refine.
> It is not something that the program phenix.reduce can perdeuterate as it
> is an unusual position. it actually perdeuterates all the rest of the
> protein successfully.
> Does anyone have an idea how to proceed?
> i tried so far to rename the residue and give .cif restraints generated
> with readyset for the new tautomer. phenix seemed to recognised it  but it
> failed due to the fact it does not recognise the residue as being a residue
> to link to the other residues and bounds bounce off. A friend told me a
> cif_link was the problem. Then i tried to apply cif_modification in a
> parameter file with the corresponding .cif file as explained briefly on:
> http://www.phenix-online.org/documentation/refinement.htm#anch88
> it does not solve the problem. the link between the new tautomer residue
> and the rest of the residues does not occur in refinement.
> Thanks for your help in advance. i am getting deseperate.
> Maxime
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