[phenixbb] pseudo-translational symmetry refinement

a a oldclifford at yahoo.com
Tue Apr 29 14:08:23 PDT 2008

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?

Zhiyong Ren,
MD Anderson Cancer Center

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