[phenixbb] pseudo-translational symmetry refinement

Peter Zwart PHZwart at lbl.gov
Tue Apr 29 14:25:07 PDT 2008


Your translation on (0,0,0.5) is indeed the cause for the intensity
stats looking differnt then 'normal' data.
What are your R-values? Is your unit cell 'full'? i.e. is the packing
such that  a connected network of molecule exists such that the
crystal doesn't fall apart?



>   - <I^2>/<I>^2 : 2.519
>   - <F>^2/<F^2> : 0.724
>   - <|E^2-1|>   : 0.854
>   - <|L|>, <L^2>: 0.504, 0.337

>  Patterson analyses
>   - Largest peak height   : 67.742
>    (corresponding p value : 4.897e-06)
>  -------------------------------------------------------------------------------
>  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?

[a hidden ps, trying not to offend anyone]:

In general, one should 'treat' the target function in refinement
rather than the data. Randy has done some work on developing specific
target functions / adapters for refinement with translational
symmetry, but that is not yet in a production stage as far as I can

If 'treating' merged data and using it in refinement would be
acceptable, I propose we modify Fobs according to the following rule,
producing lower R-values:

Fobs-treated = Fobs - (Fobs-Fcalc)*beta

Where beta is a parameter of choice between 0 and 1, beta will reflect
the confidence of the researcher in her/his structure.

This clearly seems unacceptable to me, unless beta is set to zero ...

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