[phenixbb] Question about unrestrained refinement

Louis Lazar louisl at brandeis.edu
Mon Jan 9 10:30:41 PST 2012

Hello all,

I had a question about unrestrained refinement. I have several data sets
(right near 1 A resolution) that are nearly fully refined, but to finish I
would like to run one round of unrestrained refinement. At this point, I
want to focus on unrestrained refinement of just the protein, and not any
waters. How would the syntax for refining just the chains of the protein
(and not water) look in the command line? I also want to include
anisotropic refinement of B-factors in this last refinement run.

Should it look something like:
strategy=individual_sites+occupanices+individual_adp \
adp.individual.anisotropic="not water and not element H" wc=0 wu=0

Then what should I add after this to include just my protein chains and
omit waters from the unrestrained refinement?

Also, if I wanted to not refine the waters at all in this round of
refinement, what should I add to the command line to make that happen?

Thank you in advance as always.


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