[phenixbb] pseudo-translational symmetry refinement

[Stephen Graham]

Question for the experts:

In a case like this with strong translational NCS, might one get value
from using a least squares refinement target rather than maximum
likelihood?  As far as I understand it (which ain't so far) I would
assume that least squares would be less influenced by the systematic
variation in intensities of the reflections than maximum likelihood
would.

I note that phenix.refine has the option of least squares "target =
*ml mlhl ml_sad ls".  Can anyone comment on whether this has helped
the refinement in cases with translational NCS?  (I myself have been
luck enough to avoid such cases thus far!)

Cheers,

Stephen

On 4/30/08, Paul Adams <PDAdams at lbl.gov> wrote:
> Hi,
>
>     the presence of this level of translational NCS (which you should
>  be able to see from the arrangement of your molecules) is likely to
>  lead to some issues with refinement. You will have sets of strong and
>  very weak reflections. In this case you are likely to see poorer R-
>  factors than you otherwise might expect at the same resolution (as
>  there will be a lot of noise associated with the very weak
>  reflections). However, you don't say what the R-factors are though.
>
>    Cheers,
>         Paul
>
>
>  On Apr 29, 2008, at 2:08 PM, a a wrote:
>
>  > Dear all:
>  > We have a set of crystal data having psuedo-translational symmetry
>  > when examined with xtriage:
>  > ----------------------------------------------------------------------
>  > ---------
>  > Twinning and intensity statistics summary (acentric data):
>  >
>  > Statistics independent of twin laws
>  >   - <I^2>/<I>^2 : 2.519
>  >   - <F>^2/<F^2> : 0.724
>  >   - <|E^2-1|>   : 0.854
>  >   - <|L|>, <L^2>: 0.504, 0.337
>  >        Multivariate Z score L-test: 1.854
>  >        The multivariate Z score is a quality measure of the given
>  >        spread in intensities. Good to reasonable data are expected
>  >        to have a Z score lower than 3.5.
>  >        Large values can indicate twinning, but small values do not
>  >        necessarily exclude it.
>  >
>  >
>  > No (pseudo)merohedral twin laws were found.
>  >
>  >
>  > Patterson analyses
>  >   - Largest peak height   : 67.742
>  >    (corresponding p value : 4.897e-06)
>  >
>  >
>  > The analyses of the Patterson function reveals a significant off-
>  > origin
>  > peak that is 67.74 % of the origin peak, indicating pseudo
>  > translational symmetry.
>  > The chance of finding a peak of this or larger height by random in a
>  > structure without pseudo translational symmetry is equal to the
>  > 4.8972e-06.
>  > The detected tranlational NCS is most likely also responsible for
>  > the elevated intensity ratio.
>  > See the relevant section of the logfile for more details.
>  > The results of the L-test indicate that the intensity statistics
>  > behave as expected. No twinning is suspected.
>  >
>  > ----------------------------------------------------------------------
>  > ---------
>  > The structure was solved by auto-sad at 2.7A. However, the r-factor
>  > can not be lowered by phenix.refine (TLS+ADP+rigid). Is there any
>  > manipuliations we can do to deal with this situation?
>  > Thanks,
>  >
>  > Zhiyong Ren,
>  > MD Anderson Cancer Center
>  >
>  >
>  >
>  >
>  >
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>
> --
>  Paul Adams
>  Deputy Division Director, Physical Biosciences Division, Lawrence
>  Berkeley Lab
>  Adjunct Professor, Department of Bioengineering, U.C. Berkeley
>  Vice President for Technology, the Joint BioEnergy Institute
>  Head, Berkeley Center for Structural Biology
>
>  Building 64, Room 248
>  Tel: 510-486-4225, Fax: 510-486-5909
>  http://cci.lbl.gov/paul
>
>  Lawrence Berkeley Laboratory
>  1 Cyclotron Road
>  BLDG 64R0121
>  Berkeley, CA 94720, USA.
>
> --
>
>
>
>
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-- 
Dr Stephen Graham
Nuffield Medical Fellow
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford OX3 7BN
United Kingdom
Phone: +44 1865 287 549