Thanks a lot.
Ed
Eaton E. Lattman, Ph.D.
Dean of Research and Graduate Education
Professor of Biophysics
Zanvyl Krieger School of Arts and Sciences
410.516.8215 (voice); 410.516.4100 (fax)
Mail address:
Johns Hopkins University
3400 North Charles Street
237 Mergenthaler Hall
Baltimore, MD 21218
On Jan 22, 2007, at 5:11 PM, Randy J. Read wrote:
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.
