On Thu, Nov 13, 2014 at 6:46 AM, Joseph Brock <joseph.brock@ki.se> wrote:

1. In the associated publication (Burnley et al. eLife 2012;), the ensemble refinement is validated by comparing the correlation of the ensemble generated map, with the map generated from the experimental phases for PDB entry 1YTT... I am confused how one computes an experimentally phased from structure factors deposited in the PDB that contain only anomalous intensities/amplitudes and not Hendrickson-Lattman coefficients. Is there a program within the phenix package that can do this?

AutoSol can be used to re-solve such datasets, although in the case of 1YTT it requires additional information that wasn't deposited.

Is it possible to include experimental phases during the rolling average refinement process and could this be beneficial (if the phases were of a sufficient quality)?

It is possible, but completely untested aside from verifying that it doesn't crash. I added this a year ago at the request of another user but haven't looked into it since.

3. What is the function of the "nproc" keyword? If this is the number of CPU cores that can be used in parallel, what is the most efficient way of using phenix.ensemble_refinement on a cluster?

The only parallelization is in the optimization of the ptls parameter - i.e. if you try N values for ptls, you can run N jobs at once. For a single ptls it will run in serial. So on a cluster, you are better off running N different jobs separately.

Finally, I noticed that I cannot run phenix.ensemble_refinement using a "my_parameters.eff" file, it is necessary to type on the command line.

That sounds like a bug...

-Nat