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

Maxime Cuypers cuypers at ill.fr
Thu Oct 27 02:58:10 PDT 2011

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

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:

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.

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