[phenixbb] Difference between .eff and .def?

Folmer Fredslund folmerf at gmail.com
Sun Sep 20 10:57:55 PDT 2009

Dear Maia,

I think this is documented...

Briefly, when you run phenix.refine "the first time" e.g. like this
phenix.refine mymodel.pdb mydata.mtz
the parameters used in this refinement is written to an eff
(effective) parameter file. In this case this would be something like
Furthermore a def (definition) file for the next run is generated.

Now, if you wanted to include water refinement you could
phenix.refine mymodel_refine_002.def ordered_solvent=true

and thus generating mymodel_refine_002.eff which will include the
information you provided on the commandline.

The short answer:
Yes, you can just edit the .eff file and use that in refinement.

Best regards,
Folmer Fredslund

2009/9/20 Maia Cherney <chern at ualberta.ca>:
> Hi,
> Why do we need both files .eff and .def? Can we edit the .eff file and
> use it the next round of refinement?
> Maia
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list