Dear Maia,
I think this is documented...
http://www.phenix-online.org/documentation/refinement.htm#anch8
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
mymodel_refine_001.eff
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
Hi, Why do we need both files .eff and .def? Can we edit the .eff file and use it the next round of refinement?
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