On Sep 9, 2008, at 8:12 AM, Phoebe Rice wrote:
Thanks for all the interesting answers so far!
The anisotropy issue is one that got me worrying about
truncate for data from DNA-containing crystals in
particular - and the fact that since its a default in ccp4i,
new people have stopped worrying about whether or not they
should use it.
The DNAs usually stack end-to-end, and thus are very often
aligned with a particular axis. Since all those nice flat
bases are ~3.4A apart, there are often whomping spots in
only one direction at ~3.4A (even if the DNA isn't even half
the total scattering mass). So even if the overall
diffraction limits are roughly isotropic, in certain
resolution shells isotropy is still a bad assumption.
Phoebe
We have a similar phenomenon with RNA, even if it is more globular.
If I refine with phenix.refine on I's rather than F's, and avoid
truncate, I have noticed the maps look slightly different. In one
case the Mn cluster at 2.0 Å resolution is better defined in the
sigmaA-weighted 2Fo-Fc map made from truncate/refmac than it is in the
sigmaA-weighted 2Fo-Fc map made from phenix.refine.
I wonder if truncate is actually helping more than hurting in this case?
