[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.
Pavel
More information about the phenixbb
mailing list