[phenixbb] den refinement

Jeff Headd jjheadd at lbl.gov
Tue Jun 11 09:37:15 PDT 2013

In phenix.refine you control simulated annealing that way, but
phenix.den_refine is a specialized protocol which takes advantage of much
of the phenix.refine machinery while controlling most things through the
'den' scope. It's a bit of a hack, but it was the fastest way to pull a
prototype together. You'll definitely have annealing cycles without turning
them on in the main scope, so long as 'den' is selected as a strategy
(which is is by default).

If you ran the main version of simulated annealing you would add annealing
cycles which didn't take avantage of the DEN network update steps, which is
counter to how each cycle is meant to run.


On Tue, Jun 11, 2013 at 12:06 PM, Andreas Förster <docandreas at gmail.com>wrote:

> I do indeed.  I thought I control simulated annealing through this?  If I
> turn this off, will I still get simulated annealing, activated through DEN?
> Thanks.
> Andreas
> On 11/06/2013 4:54, Jeff Headd wrote:
>> Hi Andreas,
>> My guess is that you have main.simulated_annealing=True also active in
>> your parameter file. You need to set this to False, and then the
>> refinement should proceed.
>> Jeff
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