On Thu, Sep 1, 2011 at 9:25 AM, Jose Arcadio
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. -Nat