Re: [ccp4bb]: scale failure

[Edward Berry <eaberry@lbl.gov>]

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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?

Ed
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Edward A. Berry, MailStop 3-250
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