Dear Prof. Read,<br><br>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 refinement ? <br>
<br>Peter.<br><br><br><div class="gmail_quote">On Thu, Sep 10, 2009 at 2:31 PM, Randy Read <span dir="ltr"><<a href="mailto:rjr27@cam.ac.uk">rjr27@cam.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
Yes, the data used in the Phaser map coefficients have been rescaled<br>
to remove the anisotropy, so the map should look more isotropic than<br>
the one you get from running SIGMAA. But note that neither program<br>
does a proper bulk solvent correction.<br>
<br>
Until recently (e.g. in version 2.1.4 of Phaser), the rescaling was<br>
done so that the overall average falloff of diffraction was preserved,<br>
i.e. the weakest direction was scaled up and the strongest direction<br>
was scaled down. However, we were inspired by a paper from Mike<br>
Sawaya to look at this again. He showed some convincing results that<br>
the maps are more interpretable if the weak data are all scaled up to<br>
the falloff of the strongest direction, and the tests we did agreed<br>
with this. So that is the behaviour you'll get in recent nightly<br>
builds. This agrees with your worry that the scaling could diminish<br>
the strongest reflections too much, as happened in the older versions<br>
of Phaser.<br>
<br>
I hope that helps!<br>
<br>
Regards,<br>
<br>
Randy Read<br>
<div><div></div><div class="h5"><br>
On 10 Sep 2009, at 12:58, Peter Grey wrote:<br>
<br>
> Dear Phenix users,<br>
><br>
> I have a very anisotropic data as phaser reports anisotropic deltaB<br>
> = 60.2. I would be grateful for advice of several issues.<br>
> 1.Could you please tell me if phaser map coefficients FWT,PHWT take<br>
> into account the anisotropic scaling ?<br>
> 2.This means that these coefficients will be different from those<br>
> calculated from a partial model in sigmaa because sigmaa has no<br>
> anisotropic scaling (and no bulk solvent correction) ?<br>
> 3.In the case of such severe anisotropy can the scaling diminish too<br>
> strongly the well measured high resolution reflections ? If so<br>
> should I calculate the coefficients my self by sigmaa and not use<br>
> pahser mtz output or is there a better solution ?<br>
><br>
> Many thanks in advance for sharing your thoughts and experience,<br>
><br>
> Peter.<br>
><br>
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<br>
------<br>
Randy J. Read<br>
Department of Haematology, University of Cambridge<br>
Cambridge Institute for Medical Research Tel: + 44 1223 336500<br>
Wellcome Trust/MRC Building Fax: + 44 1223 336827<br>
Hills Road E-mail: <a href="mailto:rjr27@cam.ac.uk">rjr27@cam.ac.uk</a><br>
Cambridge CB2 0XY, U.K. www-<br>
<a href="http://structmed.cimr.cam.ac.uk" target="_blank">structmed.cimr.cam.ac.uk</a><br>
<br>
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