Hi,

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,
Pavel.

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 <[email protected]>
To: [email protected]
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
_______________________________________________
phenixbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________
phenixbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb
  