![](https://secure.gravatar.com/avatar/c9876b17133228f1c4fbf5e406f80daa.jpg?s=120&d=mm&r=g)
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. Andreas 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