> -----Original Message-----
> From: [log in to unmask]
> [mailto:[log in to unmask]] On Behalf Of Eleanor Dodson
> Sent: 30 May 2007 10:16
> To: Schubert, Carsten [PRDUS]
> Cc: [log in to unmask]
> Subject: Re: [ccp4bb] How to determine ligand binding from
> diffraction pat tern?
>
> 2) There is a lot of unnecessary and confusing molecular
> replacement done.
> If your ligand data is reasonably isomorphous ( similar cell
> and space
> group) then the berst procedure is to start from your known structure
> and do rigid body refinement first to correct for any small
> changes of cell.
> If you do a full blown MR run you are very likely to get a
> solution on a
> different origin - this is formally correct but makes it hard
> to overlap
> the maps!
Often, even with soaked ligands the cell dimension changes are not
small, e.g. I've seen up to 10%, and in many cases RB refinement simply
doesn't work, even if you cut the resolution to say 4 Ang (which you
would hope should increase the radius of convergence).
But it's indeed totally unnecessary, and for the reasons you mention
actually undesirable to do a full MR search. With Phaser for example in
'Brute Force' mode you can do 'ROTATE AROUND EULER 0 0 0 RANGE r' and
'TRANSLATE AROUND ORTHOGONAL POINT 0 0 0 RANGE d' (e.g. r = 10 deg, d =
5 Ang should normally do the trick). This does a limited search around
the origin (and is also much quicker than a full BF search!!).
-- Ian
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