I would like to have some comments on whether the maps before or after
truncation are better . (obviously the Rfactors will be lower for the
truncated data ..)
I suspect it iwill be completely anecdotal - but I confess to a gut
unhappiness about throwing out measurements..
Pavel Afonine wrote:
This is why phenix.refine by default outputs both maps: 2mFo-DFc
"filled" and not "filled", and it is the best to look at both keeping
in mind all pros and cons of each of them.
On 9/15/09 5:22 PM, Peter Zwart wrote:
Application of a elliptical resolution boundary is justified because
resolution boundary from common integration programs (Denzo and
example) is spherical where diffraction for anisotropic data is
A spherical boundary would result in the inclusion of numerous poorly
measured reflections in the higher resolution shells which
these data more noisy. Imposing an ellipsoidal resolution boundary is
equivalent to removing noise from the higher resolution bins and is
the anisotropic equivalent of the normal resolution limit truncation.
Please be careful in interpreting maps from elliptically truncated
maps, there is a potential for introducing some bias. In Refmac (as
well and Phenix) maps are produced that fill in missing amplitudes
with DFcalc. When your mtz file contains only a small fraction of
miller indices in the highest (spherical) shell, all the missing
reflections will be assigned DFcalc. Depending on your anisotropy,
this can be a significant number of reflections.
I'm not sure how serious this issue is, but it might be worthwhile
checking the 'unfilled' maps as well (both phenix.refine and Refmac
allow you to compute these).