I would be worried by a structure with these R values, whether or not there is anisotropy to consider.
Several times when this has happened to me the spacegroup turns out to be wrong. You do not give any details of the solution but especially if there is some non-crystallographic translation you can assign the space group wrongly - get a MR solution which fits some of the amplitudes perfectly ( eg h k 2l, and the rest approximately so the maps look reasonable. Have you run MR in all possible spacegroup for your point group? Eleanor On 13 October 2017 at 22:08, Gerard Bricogne <g...@globalphasing.com> wrote: > Dear Randy, > > On Fri, Oct 13, 2017 at 04:11:44PM +0100, Randy Read 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. > > Your "unfortunately" calsue may be the case with the UCLA server, > but your statement is not true about what the STARANISO server (or > STARANISO as invoked within autoPROC) does: as I already indicated in > a reply to you a few months ago in this BB, the version of TRUNCATE in > STARANISO applies the French & Wilson procedure with a prior Wilson > probability whose expectation value for the intensity is modulated by > the anisotropy of the dataset. This is clearly explained on the server > - see > > http://staraniso.globalphasing.org/staraniso_about.html#step16 > > > With best wishes, > > Gerard. > > -- > > 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 > > -- > > =============================================================== > * * > * Gerard Bricogne g...@globalphasing.com * > * * > * Global Phasing Ltd. * > * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * > * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * > * * > =============================================================== >
