Wouldn't the desirability of this depend on the extent to which the
molecule has moved between the high-resolution and low-resolution
datasets ? I would have thought that there was an effective information
transfer between R-work and R-free once the rigid body movements became
too large, which might provide one with an over-optimistic idea of what
the R-free would be with the high-resolution model with the
low-resolution data.
Phil
Princeton NJ
Edward A Berry wrote:
Even if the free-R set is not preserved for the new crystal,
R and R-free tend to diverge rapidly once any kind of
fitting with a low data/param is performed, so I think
the new structure must not have been refined much beyond
rigid body (and over-all B which is included in any kind
of refinement). And that choice may be well justified.
Ed
cdekker wrote:
Hi,
Your reply to the ccp4bb has confused me a bit. I am currently
refining a low res structure and realise that I don't know what to
expect for final R and Rfree - it is definitely not what most people
would publish. So the absolute values of R and Rfree are not telling
me much, the only gauge I have is that as long as both R and Rfree are
decreasing I am improving the model (and yes, at the moment that is
only rigid body refinement).
In your email reply you suggest that even though a refinement to
convergence that will lead to an increased Rfree (and lower R? - a
classic case of overfitting!) would be a better model than the
rigid-body-refined only model. This is what confuses me.
I can see your reasoning that starting with an atomic model to solve
low-res data can lead to this behaviour, but then should the solution
not be a modification of the starting model (maybe high B-factors?) to
compensate for the difference in resolution of model and data?
Carien
On 4 Jun 2007, at 19:38, Edward A Berry wrote:
Ibrahim M. Moustafa wrote:
The last question: In the same paper, for the complex structure R
and Rfree are equal (30%) is that an indication for improper
refinement in these published structure? I'd love to hear your
comments on that too.
Several times I solved low resolution structures using high resolution
models, and noticed that R-free increased during atomic positional
refinement. This could be expected from the assertion that after
refinement to convergence, the final values should not depend on
the starting point: If I had started with a crude model and refined
against low resolution data, Rfree would not have gone as low as the
high-resolution model, so if I start with the high resolution model
and refine, Rfree should worsen to the same value as the structure
converges to the same point.
Thinking about the main purpose of the Rfree statistic, in a very
real way this tells me that the model was better before this step
of refinement, and it would be better to omit the minimization step.
Perhaps this is what the authors did.
On the other hand it does not seem quite right submit a model that
has simply been rigid-body-refined against the data- I would prefer to
refine to convergence and submit the best model that can be supported
by the data alone, rather than a better model which is really the model
from a better dataset repositioned in the new crystal.
Ed
