[phenixbb] individual_sites_real_space?
Pavel Afonine
PAfonine at lbl.gov
Wed Apr 7 11:15:43 PDT 2010
Hi Francis,
sorry for the lack of documentation on this subject. I will add it soon.
Here is a16 pages of summary about real-space refinement in general and
what's available in phenix.refine:
http://cci.lbl.gov/~afonine/rsr.pdf
Doing real-space refinement on the whole model
(individual_sites_real_space) is not very advantageous thing compared to
equivalent reciprocal-space refinement. As the above slides show, the
power of real-space refinement is that it can be done locally and
grid-search can be used (which dramatically increases convergence
radius). Often, combined real and reciprocal space refinement yields a
better model. However, I would recommend to start with
"fix_rotamers=true" option which will go residue-by-residue and fix them
locally if necessary.
Pavel.
On 4/7/10 10:30 AM, Francis E Reyes wrote:
> Phenixer's
>
>
> I just upgraded from 1.4-87 and noticed that there's
> individual_sites_real_space now. The documentation
> (http://www.phenix-online.org/documentation/refinement.htm) just shows
> that it's a parameter phenix.refine. What is this and when is it
> helpful (bad resolution/ bad model? or high resolution/good model? or
> high resolution/bad model?)
>
> Thx
>
> F
>
>
>
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
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