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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