<div dir="ltr">On Thu, Nov 13, 2014 at 6:46 AM, Joseph Brock <span dir="ltr"><<a href="mailto:joseph.brock@ki.se" target="_blank">joseph.brock@ki.se</a>></span> wrote:<br><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt"><span style="font-size:10pt">1. In the associated publication (</span><span style="font-size:8pt;font-family:AvenirLTStd;color:rgb(109,110,112)">Burnley </span><span style="font-size:8pt;font-family:AvenirLTStd;font-style:oblique;color:rgb(109,110,112)">et al. </span><span style="font-size:8pt;font-family:AvenirLTStd;color:rgb(109,110,112)">eLife
2012;</span><span style="font-size:10pt">), 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... </span><span style="font-size:10pt">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?</span><br></div></div></blockquote><div><br></div><div>AutoSol can be used to re-solve such datasets, although in the case of 1YTT it requires additional information that wasn't deposited.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt">
<div><span style="font-size:10pt">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)?</span></div></div></div></blockquote><div><br></div><div>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.</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt"><div title="Page 4"><div><div>
<div><span style="font-size:small">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? </span></div></div></div></div></div></div></blockquote><div><br></div><div>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.</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt"><div title="Page 4"><div><div>
<div><span style="font-size:10pt">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.</span></div></div></div></div></div></div></blockquote><div><br></div><div>That sounds like a bug...</div><div><br></div><div>-Nat</div></div></div></div>