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

crystallogrphy qunwan1 at gmail.com
Tue May 5 02:20:25 PDT 2015


I am doing joint X-ray and neutron refinement for my structure.

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?

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?


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