<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>I've been talking to Pavel about whether or not phenix.refine should use the same approach to the map coefficients. He's always busy implementing a lot of new things, so I'm not sure if he's had a chance to evaluate it for himself. </div><div><br></div><div>At the moment, if you want this behaviour you'll have to use F_ISO, SIGF_ISO from recent versions of Phaser. Ultimately, of course, it would be better if you used the original data in phenix.refine and it made the desired map coefficients after carrying out its own correction.</div><div><br></div><div>Regards,</div><div><br></div><div>Randy</div><div><br><div><div>On 10 Sep 2009, at 17:18, Peter Grey wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">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> </div></div>> _______________________________________________<br> > phenixbb mailing list<br> > <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br> > <a href="http://www.phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><br> <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> _______________________________________________<br> phenixbb mailing list<br> <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br> <a href="http://www.phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><br> </blockquote></div><br> _______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://www.phenix-online.org/mailman/listinfo/phenixbb<br></blockquote></div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div>------</div><div>Randy J. Read</div><div>Department of Haematology, University of Cambridge</div><div>Cambridge Institute for Medical Research Tel: + 44 1223 336500</div><div>Wellcome Trust/MRC Building Fax: + 44 1223 336827</div><div>Hills Road E-mail: <a href="mailto:rjr27@cam.ac.uk">rjr27@cam.ac.uk</a></div><div>Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk</div></span></div></span> </div><br></div></body></html>