On Jan 22 2007, Eaton Lattman wrote:
Will someone knowledgeable tell me what the present state of full 6
dimensional searches in molecular replacement?
Presumably you're referring to systematic 6D searches, not stochastic ones
like in EPMR or QoS. Do you mean "can it be done on current hardware" or
"is it worth doing"? If the former, then it's doable, though slow. In
Phaser, for instance, you can generate a complete list of rotations (using
the fast rotation function with keywords to prevent clustering and to save
all solutions), then feed that big list of rotations to the fast
translation search. In a typical problem that would probably run on a
single processor in significantly less time than the average PhD, and could
be made reasonably quick with a cluster.
If the latter, our feeling is that it isn't worth it. We've tried the full
search option on a couple of monoclinic problems (where it's only a 5D
search), and nothing came up with the full list of orientations that didn't
come up with the first hundred or so orientations.
We conclude that, even in the most recalcitrant cases, the rotation search
gives a better than random indication of whether an orientation is correct,
so it's not necessary to search through all possible orientations. However,
we do feel that it can be worthwhile to try a reasonably large number of
orientations in difficult cases.
Best regards,
Randy Read
P.S. When we generate our list of orientations, we use "Lattman" angles to
get reasonably even sampling of rotations.
