[phenixbb] Using Phenix Refine for Hypothetical Models

Sam Stampfer Samuel.Stampfer at tufts.edu
Tue Mar 5 13:48:46 PST 2013

Dear Phenix Community,

Is it possible to use phenix.refine to do simulated annealing and energy
minimization of a hypothetical model? I am currently using pyrosetta relax
for minimization; however, my hypothetical model is based on a homologous
protein whose structure is a crystallographic trimer. I would like to
preserve my model's symmetry, which I know is possible in phenix.refine but
not in pyrosetta (the symmetry controls are only supported in regular
rosetta, as far as I know).

Is there a way to have phenix ignore x-ray data and just do energy
minimization functions? How would I go about doing that? Would I need a
file containing fake/dummy x-ray data?

Thanks for your help!

-Sam Stampfer
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