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:
> [email protected]
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
> > On 13 Oct 2017, at 10:29, vincent Chaptal <[email protected]> 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
> >>> <[email protected]> (on behalf of Gianluca Cioci
> >>> <[email protected]>
> >>> )
> >>> Subject: [ccp4bb] High R/Rfree after MR
> >>> To:
> >>> [email protected]
> >>>
> >>>
> >>> 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
--
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