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I'd like to add that the value of a molecular replacement solution tends to be inversely correlated with the effort needed to find the solution. In other words, the harder you have to work to find the MR solution the less informative the phase information you tend to get. When you have very high resolution and/or NCS you may still be able to solve the structure. However, in cases were the search model is only distantly related to the protein of interest and Phaser can't find the solution, the solution may not be worth finding and you're better of focussing on getting experimental phases. Bart 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. >