Re: [ccp4bb] How to determine ligand binding from diffraction pat tern?

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: Jhon Thomas jhon1 {- dot -} thomas {- at -} GMAIL {- dot -} COM
Date: 2007-05-30

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Subject: Re: How to determine ligand binding from diffraction pat tern?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-05-30

> -----Original Message-----
> From: owner-ccp4bb@jiscmail.ac.uk
> [mailto:owner-ccp4bb@jiscmail.ac.uk] On Behalf Of Eleanor Dodson
> Sent: 30 May 2007 10:16
> To: Schubert, Carsten [PRDUS]
> Cc: CCP4BB@jiscmail.ac.uk
> 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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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: CCP4 GUI always show the job starts
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Date: 2007-05-30

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