Now it would be interesting to refine this structure to convergence,
with the original free set. If I understood correctly Ian Tickle has
done essentially this, and the Free R returns essentially to its
original value: the minimum arrived at is independent of starting
point, perhaps within limitation that one might get caught in a
different false minimum (which is unlikely given the miniscule changes
you see). If that is the case we should stop worrying about
"corrupting" the free set by refining against it or even using it
to make maps in which models will be adjusted.
This is a perennial discussion but I never saw the report that
in fact original free-R is _not_ recoverable by refining to
convergence.
Phil Evans wrote:
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
Now it would be interesting to refine this structure to convergence,
with the original free set. If I understood correctly Ian Tickle has
done essentially this, and the Free R returns essentially to its
original value: the minimum arrived at is independent of starting
point, perhaps within limitation that one might get caught in a
different false minimum (which is unlikely given the miniscule changes
you see). If that is the case we should stop worrying about
"corrupting" the free set by refining against it or even using it
to make maps in which models will be adjusted.
This is a perennial discussion but I never saw the report that
in fact original free-R is _not_ recoverable by refining to
convergence.
Indeed, perhaps we worry too much about such things.
On 14 Oct 2011, at 21:35, Nat Echols wrote:
On Fri, Oct 14, 2011 at 1:20 PM, Quyen Hoang<[email protected]> 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
