[phenixbb] neutron refinement of protonated Glu and residues with alternate conformation

Nigel Moriarty nwmoriarty at lbl.gov
Tue May 5 09:26:34 PDT 2015

On Tue, May 5, 2015 at 2:20 AM, crystallogrphy <qunwan1 at gmail.com> wrote:

> I found a few residues with two alternate conformations. After I generated
> alternation conformations, I used phenix.readyset to generate hydrogen and
> deuterium atoms for D/H atoms. However, phenix.readyset only gives H atoms
> for exchangable H atoms, such as the amide H atoms. The reason is that A
> and B letters have been assigned for the alternate conformation, not for
> the D/H atoms for particular conformations.
> Could anyone know how to solve this problem?

ReadySet! is not able to add D/H onto alternative locations. That needs to
be done with care to ensure that the correct atoms are "seeing" the correct
atoms in the surrounding environment.

> The second question is that I found one Glu residue is protonated at OE1
> atom of its carboxylate side chain. How could I generate protonated Glu? Do
> I need a strain file for this?

The restraints should happen automatically in refinement if you have the
correctly named atoms in the correct location. You can check this in the
.geo file.

I'm happy to assist if you send me the model, off-line.



Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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