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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Dear Phenix community,
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<div>I was hoping that some of you may be able to clarify some questions about Phenix.ensemble_refinement:</div>
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<div>1. In the associated publication (<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-family: Avenir; font-size: 9pt;">The
overall correlation coefficient between the electron-density map from the ensemble model (obtained without experimental phases) and the experimentally phased electron-density map was 0.903, compared with 0.873 and 0.895 for the published and re-refined single
structures. These seemingly small improvements in over- all quality indicators allow for significant local improvements.")</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></div>
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<div><span style="font-size: 10pt;">In addition, the phenix.ensemble_refinement keywords include: </span></div>
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<li class="phil-param phil-scope" style="clear: both; padding: 5px;"><span class="phil-name" style="font-weight: bold;">experimental_phases</span>
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<li class="phil-param" style="clear: both; padding: 5px;"><span class="phil-name">file_name</span><span class="phil-words" style="color: red;"> = None</span></li><li class="phil-param" style="clear: both; padding: 5px;"><span class="phil-name">labels</span><span class="phil-words" style="color: red;"> = None</span></li><li class="phil-param" style="clear: both; padding: 5px;"><span class="phil-words" style="color: red;"><br>
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<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>
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<div><font size="2">2. Is the correct procedure in parameter optimisation to optimise pTLS, then temperature offest and then tx? Or is it possible that the best ensemble may be generated from any (non-directional) combination of the above parameters? </font></div>
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<div><font size="2">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? </font></div>
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<div><font size="2">4. Can anybody suggest a good way to compare the ensembles generated by phenix.ensemble_refinement with the trajectories of traditional MD simulations (for e.g. produced by NAMD? ;)</font></div>
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<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>
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<div><span style="font-size: 10pt;">Alternatively, the queueing system for the supercomputer I use is managed by SLURM, however, I cannot submit batch jobs via the appropriate command sbatch with anything other than default parameters (keywords in a parameters.eff
or that are typed explicitly following the mycoords.pdb mydata.mtz myrestraints.cif files are not incorporated into the resulting parameters of the .log file). </span></div>
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<div><span style="font-size: 10pt;">Could these issues be due to my local environment setup?</span></div>
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<div><span style="font-size: 10pt;">I am running Phenix 1.9-1692 </span>Platform: intel-linux-2.6-x86_64 redhat-e6.5.</div>
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<div>Sorry for the long email and many thanks in advance for you help!</div>
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<div>Best regards,</div>
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<div>Joseph.</div>
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<div style="margin:0px"><font face="Courier New" size="2"><span lang="en-GB">Joseph Brock |</span><span lang="en-GB"> PhD</span><span lang="en-GB"><br>
Division of Physiological Chemistry II</span><span lang="en-GB"><br>
Department of Medical Biochemistry and Biophysics </span><span lang="en-GB"><br>
Karolinska Institutet</span><span lang="en-GB"><br>
Scheeles v�g 2</span><span lang="en-GB"><br>
SE-171 77 Stockholm, Sweden</span></font></div>
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