Re: [phenixbb] very weak reflections

Thanks for the suggestion. My original question was that the phenix refines the isoalloxazine ring as a flat plane whereas refmac refines it bent. (Same cif file) And the density fits the shape produced by each program. I guess, I should tighten restraints in refmac and see if it can make the plane and look at the difference map. Maia ----- Original Message ----- From: "Dale Tronrud" To: "PHENIX user mailing list" Sent: Thursday, December 10, 2009 4:10 PM Subject: Re: [phenixbb] very weak reflections

This is true for bond lengths and angles, but a bent isoalloxazine ring can be identified at much lower resolution because the shifts on the edges of the ring system will be large and correlated. I recommend that you try a null hypothesis test. Force the rings to be planar with a high weight. If the final difference map indicates that the edges need to be moved you have solid evidence that the ring system is bent. If the difference map is featureless then the bending is smaller than your data can detect.

Dale Tronrud

Paul Adams wrote:

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Yes, you need very high resolution data (at least 1.5A or better) to determine small molecule geometry from a crystallographic experiment.

On Dec 10, 2009, at 2:10 PM, chern wrote:

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Thank you for you reply. My problem is that I want to determine the chemistry of my molecules. The isoalloxazine ring of the FAD cofactor can be planar or bent, depending on the oxidation state, the other ligands also can be both. But it looks like I don't have high enogh resolution to see that for sure.

Maia

----- Original Message ----- From: "Paul Adams" To: "PHENIX user mailing list" Sent: Thursday, December 10, 2009 11:45 AM Subject: Re: [phenixbb] very weak reflections

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Phenix.refine includes weak reflections in refinement. If you have negative intensities in our data I suggest using the Truncate procedure (available in CCP4) to convert these to positive amplitudes.

The issues you mention with regard to ligands and FAD are most likely due to the geometry restraints used - you should look into using phenix.elbow to create restraints if you are obtaining results that don't fit what you know about the chemistry of the molecules.

On Dec 10, 2009, at 10:38 AM, chern wrote:

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Hi Pavel, Now that Randy sent you a reference about the effect of very weak reflections will you include the changes in the refiment procedure? I am wondering about that because I get different maps from the phenix refinement and from the refmac refinement. In one case I see the isoalloxazine ring of the FAD cofactor flat, in the other case this ring is bent. The same story with the densities for ligands. Is it about geometry restraints or effects of exclusion of very weak reflections?

Maia

----- Original Message ----- From: Pavel Afonine To: PHENIX user mailing list Sent: Thursday, December 10, 2009 9:31 AM Subject: Re: [phenixbb] refinement

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:

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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: [email protected] To: [email protected] 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 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.

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