[phenixbb] Phaser and anisotropy question
petgxray at gmail.com
Thu Sep 10 09:18:15 PDT 2009
Dear Prof. Read,
Thank you very much. Will this improved anisotropic scaling be implemented
in other modules of phenix.refine ? If not do you advise using F_ISO,
SIGF_ISO from the newer version of phaser as the input labels for
On Thu, Sep 10, 2009 at 2:31 PM, Randy Read <rjr27 at cam.ac.uk> wrote:
> 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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> 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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