[phenixbb] refinement

[Pavel Afonine]

Hi Pei-Chun,

the target function for coordinates refinement that is used in
phenix.refine is following:

T = wxc_scale * wxc * Txray + wc * Trestraints

where: wxc is determined automatically, wc =1 by default, and wxc_scale
= 0.5 by default. A user can adjust wxc_scale or wc.

Responding your question about "put much more weight on geometry
restraints": you can do it either by decreasing wxc_scale or by
increasing wc. I would try an array of values for wxc_scale to see which
one gives the best result.

Please let me know if it's still not clear or if you have any other
questions!

Pavel.


On 12/10/09 7:38 AM, Pei-Chun Lin wrote:
> Hi,
>
> When talking about "put much more weight on geometry restraints to
> avoid overfitting", what wxc and wxu value will you suggest to use for
> a 4A structure?
> I am working on a 3.5A structure and have no experience of adjusting
> weight value before. Any suggestion will be very helpful to me.
>
>
> PC
>
>
> ------------------------------------------------------------------------
> Date: Tue, 8 Dec 2009 20:12:29 -0800
> From: PAfonine at lbl.gov
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] refinement
>
> 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 <rwgk at cci.lbl.gov>
>     <mailto:rwgk at cci.lbl.gov>
>     *To:* phenixbb at phenix-online.org <mailto: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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