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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?