[phenixbb] Phaser and anisotropy question

Randy Read rjr27 at cam.ac.uk
Thu Sep 10 05:31:09 PDT 2009


Yes, the data used in the Phaser map coefficients have been rescaled  
to remove the anisotropy, so the map should look more isotropic than  
the one you get from running SIGMAA.  But note that neither program  
does a proper bulk solvent correction.

Until recently (e.g. in version 2.1.4 of Phaser), the rescaling was  
done so that the overall average falloff of diffraction was preserved,  
i.e. the weakest direction was scaled up and the strongest direction  
was scaled down.  However, we were inspired by a paper from Mike  
Sawaya to look at this again.  He showed some convincing results that  
the maps are more interpretable if the weak data are all scaled up to  
the falloff of the strongest direction, and the tests we did agreed  
with this.  So that is the behaviour you'll get in recent nightly  
builds.  This agrees with your worry that the scaling could diminish  
the strongest reflections too much, as happened in the older versions  
of Phaser.

I hope that helps!


Randy Read

On 10 Sep 2009, at 12:58, Peter Grey wrote:

> Dear Phenix users,
> I have a very anisotropic data as phaser reports anisotropic deltaB  
> = 60.2. I would be grateful for advice of several issues.
> 1.Could you please tell me if phaser map coefficients FWT,PHWT take  
> into account the anisotropic scaling ?
> 2.This means that these coefficients will be different from those  
> calculated from a partial model in sigmaa because sigmaa has no  
> anisotropic scaling (and no bulk solvent correction) ?
> 3.In the case of such severe anisotropy can the scaling diminish too  
> strongly the well measured high resolution reflections ? If so  
> should I calculate the coefficients my self by sigmaa and not use  
> pahser mtz output or is there a better solution ?
> Many thanks in advance for sharing your thoughts and experience,
> Peter.
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> phenixbb at phenix-online.org
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Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
Hills Road                                    E-mail: rjr27 at cam.ac.uk
Cambridge CB2 0XY, U.K.                       www- 

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