[phenixbb] General Questions about Joint x-ray/neutron refinement

Louis Lazar louisl at brandeis.edu
Thu Jun 16 13:07:38 PDT 2011

I have been running some Joint X/N jobs, and I have some questions that
perhaps you can help me with. First, doing joint refinement gave a total of
53 waters (thanks to ordered_solvent=true), yet the electron density seems
to show that there are several more waters that are actually present
(however it should be noted that there is no nuclear density associated with
those waters, and in some cases no nuclear density associated with the 53
that were chosen by ordered_solvent=true). Should I add in manually to the
electron density what I believe are these extra waters, or simply ignore

Second, when I try to real space refine any of the residues, I get an error
message telling me about exploding atoms. What is the cause of this message,
and is it possible to real space refine any of these residues and
specifically the hydrogen atoms associated with them.

Third, during the joint refinement run, I chose to refine occupancies of all
atoms. This breaks down into several questions: A) Should I be refining
occupancies at 2.0 A resolution (of the neutron structure; 1.05A for the
X-ray)? B) How does Phenix go about refining occupancies of
hydrogen/deuterium sites? C) If the resulting occupancies result in values
of, for example, 60% deuterium and 40% hydrogen, am I to presume that
deuterium presence is significant if the nuclear density looks "good". At
what point of deuterium occupation (while examining the nuclear density),
would I say that there is likely no deuterium present (or that it is

Hopefully all of these questions make sense, and if I need to clarify
anything, please let me know. Thanks so much in advance for the help, I
appreciate it as always.


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