[phenixbb] den refinement

Jeff Headd jjheadd at lbl.gov
Tue Jun 11 10:34:14 PDT 2013

Hi Andreas,

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.

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.

I'll try to make the --dry-run flag work more sensibly with


On Tue, Jun 11, 2013 at 1:21 PM, Andreas Förster <docandreas at gmail.com>wrote:

> 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?
> Andreas
> 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
>             http://www.msf.bio.ic.ac.uk
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