[phenixbb] pseudo-translational symmetry refinement
Peter Zwart
PHZwart at lbl.gov
Tue Apr 29 14:25:07 PDT 2008
Hi,
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?
Cheers
Peter
> - <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
tell.
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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