[phenixbb] den refinement

Andreas Förster docandreas at gmail.com
Wed Jun 12 01:40:28 PDT 2013

Dear Jeff,

no worries.  I assumed the --dry_run would do more than it actually did. 
  This is fine.  It didn't take me long to fix the errors that were 
printed clearly in the log file.

Thanks for your help.


On 11/06/2013 6:34, Jeff Headd wrote:
> 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
> phenix.den_refine.
> Jeff

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