Dear all,
I'm making first steps in the desolate world of low-resolution
refinement. With dodgy 3.8A data, the magic of Phaser was able to solve
the structure of a complex by MR with its components as MR models.
Jelly-body refinement does wonders for R free. There are three issues
that I would like to get some advice on:
1) Using external restraints calculated with ProSMART improved the
structure further, but I'm worried that using restraints derived from
the structures used for MR gets me into a sinkhole of model bias.
Should it be either molecular replacement or homology restraints?
2) Do I recalculate restraints at each round of refinement? In
particular, I substantially rebuilt a surface loop that I don't want to
restrain by the model.
3) Activating map sharpening results in mtz files that look just normal
and open in coot after the typical map calculation break, but no maps
are displayed. This is independent of the sharpening factor I choose
(between 5 and 60).
Thanks for your help.
Andreas
--
Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk
