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Re: [ccp4bb]: scale failure

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Yuan Ping wrote:
> Dear all,
>      I got hexagonal crystals of a protein. My previous data show the space
> is P6122. Recenly I put one of my best crystals for data collection. The
> frame looks good (I have attached it). And I use DENZO program to index the
> data. All previous step go on smoothly, until I scale the data. The scale
> result is very bad ( Part is attached). The linear R factor is about 0.516
> and square R factor is 0.922 and the chi**2 is obviously wrong. But I
> notice that the chi**2 of each frame during process is near 1 which is OK.
> Could anyone help me to figure out the possible cause?
> Thanks a lot!
Beautiful data! (the diffraction pattern, I mean).
Chi^2 of each frame are positional (x, y) chi^2, low value indicates your 
lattice fits well. Chi^2 in scalepack (between "initial scale factors" and
"final scale factors") is scaling error, and indicates "equivalent" reflections
after scaling have very different value. Have you tried using a lower symmetry
(P6) in scalepack? (No need to re-run denzo integration with the new space group).
Maybe the true space group is P61 and the previous data were twinned with the
polar axis running both directions giving false 2-fold axes?

Another possibility is that something you did to get around the close spot spacing
interferes with accurate integration. You didn't use "overlap none", did you?

Edward A. Berry, MailStop 3-250
Lawrence Berkeley National Laboratory
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Phone: +1-510-486-4335
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e-mail: EABerry@lbl.gov