Re: [phenixbb] pseudo-translational symmetry refinement

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 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 : 2.519 - <F>^2/ : 0.724 - <|E^2-1|> : 0.854 - <|L|>, : 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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