[phenixbb] Questions about phenix.fmodel

Pavel Afonine pafonine at lbl.gov
Sun Sep 10 09:04:40 PDT 2017

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.


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