I just tried refining a "finished" structure turning off the FreeR set, in Refmac, and I have to say I can barely see any difference between the two sets of coordinates.
From this n=1 trial, I can't see that it improves the model significantly, nor that it ruins the model irretrievably for future purposes. I suspect we worry too much about these things Phil Evans On 14 Oct 2011, at 21:35, Nat Echols wrote: > On Fri, Oct 14, 2011 at 1:20 PM, Quyen Hoang <qqho...@gmail.com> wrote: > Sorry, I don't quite understand your reasoning for how the structure is > rendered useless if one refined it with all data. > > "Useless" was too strong a word (it's Friday, sorry). I guess simulated > annealing can address the model-bias issue, but I'm not totally convinced > that this solves the problem. And not every crystallographer will run SA > every time he/she solves an isomorphous structure, so there's a real danger > of misleading future users of the PDB file. The reported R-free, of course, > is still meaningless in the context of the deposited model. > > Would your argument also apply to all the structures that were refined before > R-free existed? > > Technically, yes - but how many proteins are there whose only representatives > in the PDB were refined this way? I suspect very few; in most cases, a more > recent model should be available. > > -Nat
