Thank to all for the replies ! I have tried the UCLA server using the unmerged intensities from XDS and the verdict is strong anisotropy The Rfactors (after Phaser+Refmac) are only slightly lower for the Corrected. Non Corrected: Corrected
R factor 0.3778 R factor 0.3732 R free 0.3871 R free 0.3816 I will make a few cycles of rebuilding and see if it makes any difference... Best regards, GIA Best regards, GIA On Fri, Oct 13, 2017 at 5:11 PM, Randy Read <rj...@cam.ac.uk> wrote: > Just to add to this point. The MR algorithms in Phaser are now able to > make better use of intensity data, which is particularly important when you > have any very weak data. Having weak data can’t be avoided when you have > serious anisotropy (or tNCS or a combination of the two). Unfortunately, > if you use amplitudes that have been through the French & Wilson (truncate) > algorithm, the real variation in intensity is partially masked because the > posterior amplitude values are computed on the prior assumption that all > the reflections in a resolution shell have the same underlying intensity > distribution. > > The UCLA server actually uses Phaser under the hood — what they add is to > turn the anisotropic B-values into suggested resolution limits in the > different directions. However, I don’t think they allow you yet to submit > intensities, which would be better. > > Best wishes, > > Randy Read > > ----- > 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: rj...@cam.ac.uk > Cambridge CB2 0XY, U.K. > www-structmed.cimr.cam.ac.uk > > > On 13 Oct 2017, at 10:29, vincent Chaptal <vincent.chap...@ibcp.fr> > wrote: > > > > Dear Gia and Paul, > > > > about anisotropy, one point to keep in mind is that it is not > necessarily linked to the difference in resolution limits. > > In fact I am at the moment working on one of these cases, with extremely > large difference in resolution limits, but relatively low anisotropy. > Anisotropy is more a deviation from "normal" intensity falloff as a > function of resolution. There is a thin difference/relationship between the > two concepts that I think is worth investigating. > > > > we have performed a statistical analysis of this phenomenon and the > paper is in revision at the moment, but if you want to know where your > anisotropy stands in respect to all the other PDBs out there, feel free to > contact me off list. > > You mention MR: Phaser calculates the anisotropy so you can find the > value in the first lines of the log. > > > > Staraniso or the UCLA server are good to test if you have anisotropy. > Staraniso has a newer way of dealing with intensity falloff and accounting > for it. > > > > All the best > > Vincent > > > > > > > > > > On 13/10/2017 10:58, Paul Miller wrote: > >> I had a similar problem to what you describe. In my case the dataset > was severely anisotropic (2.6A, 3.4A, 4.6A in each axis). The R factors > were stuck similar to yours but the map looked good. I was told by someone > with a much better appreciation of the theory than myself that the > anisotropy was causing the problem. > >> > >> It would be interesting to know from an expert in anisotropy e.g. the > creators of UCLA anisotropy server or Startaniso whether anisotropy can > cause this problem and whether there is any way around it. > >> > >> Cheers, Paul > >> > >> Paul Steven Miller (PhD) > >> Postdoctoral Researcher > >> University of Oxford > >> Wellcome Trust Centre for Human Genetics > >> Division of Structural Biology > >> Roosevelt Drive > >> Oxford > >> OX3 7BN > >> > >> > >> ---- Original message ---- > >> > >>> Date: Fri, 13 Oct 2017 10:30:22 +0200 > >>> From: CCP4 bulletin board > >>> <CCP4BB@JISCMAIL.AC.UK> (on behalf of Gianluca Cioci < > gianluca.ci...@gmail.com> > >>> ) > >>> Subject: [ccp4bb] High R/Rfree after MR > >>> To: > >>> CCP4BB@JISCMAIL.AC.UK > >>> > >>> > >>> Dear All, > >>> I am trying to refine a structure at 3.3A. Model has > >>> 60% identity to the target. Maps look OK (for 3.3A) > >>> and rebuilding in Coot is relatively > >>> straightforward. However, after some rebuilding > >>> cycles the R factors are stuck at 0.37/0.39 > >>> (REFMAC). > >>> XTRIAGE tells me that everything is normal (no twin, > >>> 98% completeness, R=3.5% in the low resolution bin), > >>> perhaps some anisotropy is present. > >>> I have already refined 2 homologous structures at > >>> resolutions going from 3.2 to 3.8 and there were no > >>> problems (final R ~ 0.21/0.24). > >>> Any advice ? > >>> Thanks, > >>> GIA > >>> > > > > -- > > Vincent Chaptal, PhD > > Institut de Biologie et Chimie des Protéines > > Drug Resistance and Membrane Proteins Laboratory > > 7 passage du Vercors > > 69007 LYON > > FRANCE > > +33 4 37 65 29 01 > > http://www.ibcp.fr > > > > >
