[phenixbb] Problem with R-free assignment

Nathaniel Echols nechols at lbl.gov
Thu Sep 1 09:47:51 PDT 2011

On Thu, Sep 1, 2011 at 9:25 AM, Jose Arcadio
<jose.farias at tuebingen.mpg.de> wrote:
> Now I did a new run of refinement using my best dataset (better statistics)
> and also including the anomalous data FP, SIGFP, DANO and SIGDANO.
> Obviously, my R-work and R-free got pretty much better.
> Nevertheless, the R-free was better than R-work at the beginning of the run,
> at the end of the refinement R-free and R-work inverted as usually (being
> R-free worst than R-work)  r_work = 0.2582  r_free = 0.2888 . Certainly,
> there was a mistake with a new assignment of the free set of reflections.
> Now I am aware that the set of free reflections has to be the same all over
> the refining procedure.
> Here are the questions
> How can I be sure that my R-free is still a safe cross validation of the
> correctness of my structure?

The behavior of R-work and R-free suggest to me that the second
dataset is isomorphous with the first - is this correct?  If so, you
can transfer the R-free flags between files using the reflection file
editor in the GUI.  It will automatically extend the original flags to
higher resolution if necessary.  I think there is also a way to do
this within phenix.refine, but I haven't tested it.

> Is it useful to perform a round of simulated annealing in order to erase any
> wrong information in my model and start the refinement rounds again?

Yes, this is the next best choice if you can't preserve the original
test set.  But you should try to copy it over first.


More information about the phenixbb mailing list