On Tue, Jul 5, 2011 at 11:17 AM, Young-Jin Cho
While I am trying to deposit, I am faced with several things that I am not sure: FYI. I am in the <Refinement Statistics> section (Auto Dep Input Tool) in the PDB bank. Most values are came from pdb file that was made from phenix.refine but it asks me "R-factor (all)" that satisfy the limits established by high & low resolution cut off and "number of unique reflections (all)". My simple question is if phenix has those kind of information, if so where I can find them.
It looks like these aren't included in the PDB header of the files phenix.refine writes. I think "R-factor (all)" is an artifact from the era when crystallographers would do a final refinement with all reflections included (a Very Bad Idea), and I think I always left this blank in PDB depositions. Assuming you didn't truncate the resolution, "Number of unique reflections (all)" is probably whatever is in the MTZ file - depending on the outlier removal, it may be slightly more than phenix.refine reports.
Another question is if I changed water (deletion or changed occupancy) based on 'precheck', should I run phenix.refine again to get R/Rfree values in correct? I am not sure if these are captured by PDB automatically or not. (seemingly they do like that at this point but not 100% sure yet.)
You can run phenix.model_vs_data or the validation GUI to determine new R-factors. Unless the PDB has made huge improvements in the last half-year, their recalculation of R-factors isn't at all robust. -Nat