[phenixbb] Problem with R-free assignment
pafonine at lbl.gov
Thu Sep 1 09:49:10 PDT 2011
DANO and SIGDANO are not used in refinement.
Resetting ADPs to an average value, and performing ~5 macro-cycles of
refinement with SA and weights optimization typically should be
sufficient. Make sure you are using the latest PHENIX version from
Let me know if you have any questions.
On 9/1/11 9:25 AM, Jose Arcadio wrote:
> Dear phenix.refine community:
> I am solving a protein structure using experimental phasing. In order
> to do that I combined two derivative isomorphous datasets into a
> double SAD experiment (to increase the individual weak anomalous power
> from each dataset) using SHARP.My resolution is 3.2 A, and the space
> group is C2221.
> I managed to build a model using the density-modified phases from
> SHARP. Then I started refining against one of my derivative datasets
> because my native dataset is non-isomorphous due to the heavy meal
> soaking.Then I made two mistakes :(
> 1. I did not realize at the beginning of my refinement-building rounds
> that I was refining against the dataset that showed the worst statistics.
> 2. I was using a dataset with only FP and SIGFP but not DANO and
> SIGDANO. I used the phases from my SHARP map (also the experimental
> phase restraints)
> 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?
> 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?
> Do you have any suggestions?
> All the best
> Jose Farias
> phenixbb mailing list
> phenixbb at phenix-online.org
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