[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
[ccp4bb]: translational NCS
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html ***
I have a pseudo translational NCS which relates the 4 mols
in the asymmetric unit by ~(0.5, 0, 0) and ~(0.25, 0.25, 0).
The 4 mols differ slightly on the domain angle as a
result of lattice packing. The resolution is 2.4 A,
and the space group is C2. MAD maps etc were not that great,
but I managed to build the model manually, and have refined
a couple of cycles so far. The 2fo-fc and fo-fc maps have
showed many new and nice features, which is encouraging,
but R/Rf is about 41/45.
Before going further with the traditional procedure,
I think I should understand a few things:
- Instead of selecting R-free set randomly, do I need to
select it specially to avoid any "correlation" of
reflections? Some papers suggest to use thin shell
selection in the presence of NCS. Is it mainly for
rotational NCS? But I have alternative layers of
strong (25%), weak (50%), and very weak (25%) data.
To make it simpler to think, if I had just (0.5, 0, 0)
translation, can I consider (2n, k, l) and (2n+1, k, l)
as "correlated"? On the other hand, this translation can
also be treated as a pseudo 2-fold rotation if the
crystallographic symmetry is considered, and this pseudo
2-fold is parallel with the crystallographic 2-fold.
So, is it ok to use thin shell then? Or for every (2n, k, l)
reflection with free flag, make the corresponding (2n+1, k, l)
also free? What if I have a combination of rotational and
translational NCS, or a translation that cannot be
turned into a rotation?
- What are people's generall experiences in the effects of
the test set selection on the outcomes of the refinement?
- At 2.4 A, is it now possible to do automatic rebuilding
with wARP/REFMAC? How about if many reflections are weak?
- When a large fraction of reflections is weak across all
resolution ranges, would the MAD map quality be largely reduced
because the weak Friedal pairs may not be accurately measured?
Thanks for any suggestions and comments,
P.S. This mighe be the third tough translational NCS case