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
