[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:


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.


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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