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The indexing convention shouldnt have changed between scalepack and your mtz conversion, but it is quite likely you have a different definition of the asymmetric unit and hence may have k.h.-l instead of h,k,l say (You dont say what the space group is..)
Oops, it's P6(3). It appears to be h,-k,l, but the indices go much higher in the .sca file (i.e. 65,-24,1 as opposed to 56, 1, 5 in the .hkl file converted from MTZ). However, the number of reflections is very similar (62491 vs. 60130) and I assume any discrepancy is due to the reflections that CCP4 claims is missing around 1.5A.
If I use SHELXPRO to create the .hkl file directly from the scalepack file, the indices do not change.
You should generate a SHELX.hkl file with the FreeR and intensities from your MTZ.
How do I do this? Do I need to run mtz2various interactively instead of through ccp4i to use the intensities? (Through the interface it only lets me output Fs.)
thanks, Nat
