But that isn't necessarily the case if the search is hard because your
search models individually constitute only a small part of the
asymmetric unit. Say that 80% of the AU consists of multiple
different proteins with known structure; the phase information would
be very high if you find the solutions.
Filip
On 1/22/07, Bart Hazes <[log in to unmask]> wrote:
> 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.
> >
>
--
Filip Van Petegem
University of California, San Francisco
Cardiovascular Research Institute
1700, 4th Street, QB3 Rm304
San Francisco
CA94158
phone: 415 514 2836
fax: 415 514 2550
email: [log in to unmask]
|