[phenixbb] refinement

Pavel Afonine PAfonine at lbl.gov
Tue Dec 8 20:12:29 PST 2009


although I've seen cases like yours when SA in Cartesian space did 
miracles, in many of cases modeling at 4A resolution is a tough problem.

Since clearly SA didn't work out (given R/Rfree ~ 37/50% and the 
starting 48/50), I would try splitting your model into rigid domains and 
refine each as a rigid body. Plus, I would refine one isotropic B per 
residue or per domain (try both). This is a few minutes to try so why 
don't you do so.
Also, I would still combine it (rigid body and B-factor refinement) with 
Cartesian SA, but I would put much more weight on geometry restraints to 
avoid overfitting.

As you probably aware of, in phenix.refine you can run combined 
refinement jobs, for example, consisting of SA, rigid body, B-factor 
refinement and so on. So I would recommend playing with the above 
suggestions to see if it works. Plus, *don't forget looking at the maps 
- may be you manage to fit something manually.*

By the way, which R-factors you get if you run:

phenix.model_vs_data data.mtz model.pdb

(phenix.model_vs_data will account for twinning (if any) using Xtriage 
automatically) ?

Write us if you have questions.

Good luck,

On 12/8/09 7:02 PM, r n wrote:
> 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.
> Ralf
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