[phenixbb] den refinement

Andreas Förster docandreas at gmail.com
Tue Jun 11 10:21:02 PDT 2013

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...

When I run phenix.den_refine --dry_run, aren't these inconsistencies and 
missed requirement supposed to be caught, or do I misunderstand things?


On 11/06/2013 5:37, Jeff Headd wrote:
> 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.
> Jeff

         Andreas Förster, Research Associate
         Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London

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