[phenixbb] Using Phenix Refine for Hypothetical Models

Nathaniel Echols nechols at lbl.gov
Wed Mar 6 07:41:31 PST 2013

On Tue, Mar 5, 2013 at 11:55 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
> Also note that geoemtry terms in phenix.refine are not designed for
> simulations, they are very basic just enough to make refinement work well,
> and almost certainly not suitable to do simulations purely based on them.
> For example there is no electrostatic terms, which means if you don't
> carefully specify secondary structure restraints your model will unfold..
> etc.

Two further points:

1) If you're trying to preserve a crystallographic trimer anyway, one
option is to set wxc_scale to a small but non-zero number, i.e.
essentially defining an envelope around your protein with the fake
data.  This will allow your model geometry to refine but limit how far
it can move.

2) The reference model restraints could also be useful here (with or
without "data").


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