As a follow-up to the question posted by Jon Winger regarding riding hydrogens, do we all agree that the current PDB format does not allow complete reconstruction of the final stage refinement? For instance, the geometry weight factor is never reported.
Second question: is it important to make sure that such reconstruction is possible? The PDB has already taken an important step in requiring experimental data deposition, so in theory I can always run my own few cycles of refinement, but we all know how often that gives you the reported Rfree. Third question: if it is important, what is the easiest way to assure it? My thinking is that the script used at the final stages of the refinement should be made available, so if you match it with the appropriate version of the software, you should in theory get the same results. Of course, with nearly 50,000 crystal structures in the PDB, the train has left the station long time ago. -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /
