<div dir="ltr">Hi Andreas,<div><br></div><div style>The --dry_run flag is designed to evaluate a phenix.refine run, and admittedly I never tested that with phenix.den_refine. That test is checking for valide phenix.refine parameters, and your inputs would check out fine.</div>
<div style><br></div><div style>In the absence of a parameter file, the den_refine routine makes the necessary changes to the default scheme (one macrocycle, assures positional refinement is active, etc.), but a phenix.refine parameter file would overwrite these and could lead to the catches that you're seeing.</div>
<div style><br></div><div style>I'll try to make the --dry-run flag work more sensibly with phenix.den_refine.</div><div style><br></div><div style>Jeff</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Tue, Jun 11, 2013 at 1:21 PM, Andreas Förster <span dir="ltr"><<a href="mailto:docandreas@gmail.com" target="_blank">docandreas@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Ok, that's fine - and it's running now. But I had to fix a number of other things: enable positional refinement, one macrocycle only...<br>
<br>
When I run phenix.den_refine --dry_run, aren't these inconsistencies and missed requirement supposed to be caught, or do I misunderstand things?<span class="HOEnZb"><font color="#888888"><br>
<br>
<br>
Andreas</font></span><div class="im HOEnZb"><br>
<br>
<br>
On 11/06/2013 5:37, Jeff Headd wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
In phenix.refine you control simulated annealing that way, but<br>
phenix.den_refine is a specialized protocol which takes advantage of<br>
much of the phenix.refine machinery while controlling most things<br>
through the 'den' scope. It's a bit of a hack, but it was the fastest<br>
way to pull a prototype together. You'll definitely have annealing<br>
cycles without turning them on in the main scope, so long as 'den' is<br>
selected as a strategy (which is is by default).<br>
<br>
If you ran the main version of simulated annealing you would add<br>
annealing cycles which didn't take avantage of the DEN network update<br>
steps, which is counter to how each cycle is meant to run.<br>
<br>
Jeff<br>
<br>
<br>
</blockquote>
<br></div><div class="im HOEnZb">
-- <br>
Andreas Förster, Research Associate<br>
Paul Freemont & Xiaodong Zhang Labs<br>
Department of Biochemistry, Imperial College London<br>
<a href="http://www.msf.bio.ic.ac.uk" target="_blank">http://www.msf.bio.ic.ac.uk</a><br></div><div class="HOEnZb"><div class="h5">
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