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 <[log in to unmask]> 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
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