On Fri, 2012-01-06 at 11:18 -0700, Francis E Reyes wrote: > I've seen the following question asked: At what resolution is > (individual,group,one per residue, two per residue,overall) > appropriate?
My personal opinion is that the individual B-factor refinement with restraints proper to the resolution is the only thing you will ever need. This thread may be interesting to you. http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg14133.html > One common response is "try a number of different B-factor refinement > protocols, use Rfree as a guide to determine which one is > appropriate". I guess this is along the lines of "B-factor refinement > being stable". Seems reasonable to me. > > However is this approach sufficient justification to address > "over-fitting at low resolution"? As a general rule, the R-free should never be the only criterion. Additional criteria will vary depending on what alternative protocols you are investigating. To try to generalize, I'd say that improved unbiased fit (via R-free) should be combined with the requirement that model parameters are physically meaningful. For example, the two-per-residue B-factor model fails miserably on that account, and my sincere wish is that it's use in modern refinement software will be obfuscated to the extent needed to render it unusable. Cheers, Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs
