Or use Kevin's csymmatch which does wonders on scrambled oligomers that (nearly always, at least in my hands) come out of Phaser in cases like those mentioned by Ian and which do need MR.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: [log in to unmask]
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Ian Tickle [[log in to unmask]]
Sent: Monday, November 21, 2011 1:02 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] LESS MR pleae.. 1.95A, different phase
On Mon, Nov 21, 2011 at 10:23 AM, Eleanor Dodson <[log in to unmask]> wrote:
> Just a plea for less molecular replacement.
>
> If you get a new crystal of a known protein with the same cell dimension as
> youur old crystal, the most likely scenario is that it has the same group,
> and you really should not try MR - use the previous solution as input to do
> rigid body refinement, and then
> a) the R factor will tell you if this is a reasonable hypothesis (it
> usually is..) and
> b) you dont have this awful problem of not being able to compare the
> solutions..
>
> Eleanor
But sometimes (or actually we find quite often) the crystal after
soaking & freezing is sufficiently non-isomorphous (we sometimes see
up tp 10% changes in cell parameters) that RBR just doesn't work, and
then you have to fall back on MR. The solution in that case to avoid
problems of generating symmetry-related and/or origin-shifted
molecules is to do a limited MR search, e.g. rotating/translating each
molecule in the a.u. independently by up to 5 deg & 5 Ang. from the
model (which of course has 100% similarity making it a lot easier).
Furthermore, because the number of points sampled is much less one can
afford to do the more accurate full 6-D search, as opposed to the
usual 3-D RF followed by 3-D TF on each RF solution. So now we do
this routinely (we don't even bother with a preliminary RBR). I
believe the limited 6-D search can be done with Phaser.
Cheers
-- Ian
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