<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>Yes, the grid optimization was turned on. Let's see if den.reference_file will help.</div><div>Thanks,<br><br>Sent from my iPod</div><div><br>On Oct 2, 2013, at 4:56 PM, Jeff Headd <<a href="mailto:jjheadd@lbl.gov">jjheadd@lbl.gov</a>> wrote:<br><br></div><blockquote type="cite"><div><div dir="ltr">Hi Jan,<div><br></div><div>Did you run your DEN refinement with optimize=True? If you haven't run the grid optimization, it's unlikely that you found the optimal gamma/weight pair for your specific case.</div>
<div><br></div><div>Also, I would recommend not using reference model restraints while running DEN refinement. This could potentially prevent your model from "deforming", if you are restraining it to be the same as a reference model.</div>
<div><br></div><div>To use a reference file with DEN, you would use:</div><div><br></div><div>den.reference_file="path_to_reference_file"</div><div><br></div><div>That will handle the chainID/resID matching automatically, and correctly use your reference in a DEN context.</div>
<div><br></div><div>Jeff</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Oct 2, 2013 at 4:43 PM, Jan van Agthoven <span dir="ltr"><<a href="mailto:janccp4@gmail.com" target="_blank">janccp4@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi everyone,<br>
I ran a DEN refinement of my low resolution structure (3.6) to improve<br>
my model. I typed in the following command:<br>
<br>
phenix.den_refine model.pdb data.mtz den.reference_file=reference.pdb<br>
reference.params<br>
<br>
with reference.params saying:<br>
<br>
refinement.reference_model.reference_group {<br>
reference = chain A and resseq 1:953<br>
selection = chain A and resseq 1:953<br>
}<br>
refinement.reference_model.reference_group {<br>
reference = chain B and resseq 1:687<br>
selection = chain B and resseq 1:687<br>
}<br>
<br>
because the reference file only contains chain A and chain B.<br>
<br>
Unfortunately I obtained much worse R factors then with a regular refinement:<br>
<br>
Start R-work = 0.2798, R-free = 0.3176<br>
Final R-work = 0.3733, R-free = 0.4089<br>
<br>
Does someone have an idea what could have go wrong?<br>
<br>
Thanks,<br>
_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
</blockquote></div><br></div>
</div></blockquote><blockquote type="cite"><div><span>_______________________________________________</span><br><span>phenixbb mailing list</span><br><span><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a></span><br><span><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a></span><br></div></blockquote></body></html>