[phenixbb] Phenix.ensemble_refinment questions

Nathaniel Echols nechols at lbl.gov
Thu Nov 13 07:53:36 PST 2014

On Thu, Nov 13, 2014 at 6:46 AM, Joseph Brock <joseph.brock at 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...

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