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Hi Ron:
I think my previous response was worded quite poorly. The essence
of the problem is that a != b in a trigonal system (unlike
hexagonal). So if you have two data sets (say a native and a
derivative) and you process each of them, there is a priori a 50%
chance that what you called "a*" for the native will be "b*" for the
derivative. Neither is really right or wrong. It is only relative to
an arbitrary reference.
Since a and b are not equivalent, it isn't simply a rotation, it
really is a reindexing. Riso for a good derivative might be about
15% when they are both indexed the same way, and shoots up to 40% or
more if indexed the "wrong" (relatively incompatible) way.
Similarly with molecular replacement, so if you are doing molecular
replacement, for example, the Fcalcs generated by ccp4 or CNS have a
50% chance of choosing "a" differently from your native data set.
I've done a lot of work in that space group in the last 12 (yikes)
years. So I've become painfully familiar with this.
There is a discussion in the CCP4 users guide in the $CCP4/manual
directory that describes this much better than I have.
HTH,
Bill
On Mar 28, 2006, at 10:12 AM, R. Stenkamp wrote:
Hi.
Your statement about the indexing issue for trigonal space groups
confused me. I've not seen ccp4 programs change the indices (unless
explicitly instructed to do so). Isn't the choice of a* and b* made
back at data processing/indexing time?
I know the indexing ambiguity makes a lot of difference when
comparing data sets, even MAD sets at different wavelengths, but
how would an indexing issue affect a molecular replacement and
refinement problem? Re-indexing of hkl corresponds to a rotation
of the reciprocal lattice, so the structure ought to be just as
readily described for the reindexed data as for the original
setting, right? Again, the problem comes when you try to compare
two structures or data sets that may differ by the rotation.
Thanks.
Ron
p.s. The a*-b* choice is also an issue in tetragonal space groups
like P4(x).
