I still don't understand how a structure model refined with all data
would negatively affect the determination and/or refinement of an
isomorphous structure using a different data set (even without doing
SA first).
Quyen
On Oct 14, 2011, at 4:35 PM, 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
