Hi David,
1. Run phenix.fmodel on a phenix-refined pdb file, and get the same FMODEL parameters as phenix.refine itself put into its output mtz file. Can I extract from the log files the scaling factors that phenix.refine used, and if so, how?
instead why not use Fmodel that is reported in MTZ file after any refinement run?
2. Run phenix.fmodel on a pdb file, and get (unscaled) FMODEL values that include bulk solvent contributions as well as the ususal atomic-based structure factors.
I think my problem arises from trying to understand the documentation at phenix-online.org/documentation/reference/fmodel.html. Specifically: the equation at the very top of the documentation states:
Fmodel = scale * exp(AnisoScale) * (Fcalc + k_sol * exp(-b_sol*s^2/4) * Fmask)
But I had thought(?) that k_sol and b_sol were no longer being used. I don't see any reference to these in my phenix.refine log files.
Indeed, k_sol and b_sol are not available. There are still tools in cctbx to obtain k_sol and b_sol. Pavel