[phenixbb] refinement

r n ramme29 at yahoo.com
Tue Dec 8 19:02:01 PST 2009

Thanks a lot.I did download the new -dev249 and did cartesian SA, R goes down to 37 but R-free (50) did not. 
Any suggestions?

From: Ralf W. Grosse-Kunstleve <rwgk at cci.lbl.gov>
To: phenixbb at phenix-online.org
Sent: Tue, December 8, 2009 3:34:09 PM
Subject: Re: [phenixbb] refinement

> I do have very low resolution data (around 4 ang), what are
> the efficient way of doing refinement, either rigid body alone or
> rigidbody and tls or individual with group_adp. I did both, but not
> much significant changes in Rfree stays around 48/50%.

You could also try Cartesian or torsion-angle simulated annealing.
I'd try both. In my experience Cartesian SA often works better even
at low resolution.
If you get errors running torsion-angle annealing, please try
the latest nightly build (dev-249) since I've fixed several
problems since the 1.5-2 release.

> Also I do have other questions
> 1. While doing rigid body refinement, phenix complaint about the
> special position and could not perform rigid body refinement,
> whereas individual site refinement is working fine. I do have to
> delete the atom in special position for rigid body refinement?

You could use
  sites.rigid_body = ...
to select the bodies you want to refine. The rest (including your
atom on the special position) will not move.

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