Re: [ccp4bb] an over refined structure

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From: David M Shechner shechner {- at -} MIT {- dot -} EDU
Date: 2008-02-04

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From: Pietro Roversi pietro {- dot -} roversi {- at -} PATH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-02-05

Subject: Re: an over refined structure
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2008-02-05

Hi Sun,

On Mon, Feb 04, 2008 at 02:15:05PM -0800, Sun Tang wrote:
> I used NCS before rigid body refinement. After that I did not put
> NCS restraints in the restrained refinement and TLS+restrained
> refinement because it raised the R/Rfree quite a lot.

Use NCS. Really!

There is never a reason for switching off NCS restraints (ok _maybe_
at real atomic or ultra-high resolution ...). Obviously, you'll need
to change the way you apply NCS restraints: from a simple per-chain
definition to maybe a per-domain definition, taking out residues in
crystal contacts, allowing for a different base B-factor of different
chains/domains etc. Some programs do these things fairly automatically
for you.

This might make it awkward to use NCS sometimes, but at 2.8A it is a
must (I think). And if your use of NCS increases Rfree, then there is
aproblem in the setup of NCS restraints, not in the principal
usage.

Note: re-introducing NCS restraints might increase the R, but if the
Rfree stays similar: who cares?

--------------------------------------------------------------

See also:

G J Kleywegt, "Use of non-crystallographic symmetry in protein
structure refinement", Acta Crystallographica, D52, 842-857 (1996).

According to

http://xray.bmc.uu.se/~gerard/citation.html

a "classic!" paper [gosh ... I really like Gerard's style ;-)].

Cheers

Clemens

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CCP4bb <-- 2008 <-- February 2008 <-- 05 February 2008

Previous message:
Subject: Re: 3D Glasses - Vuzix HMD by eDimensional
From: David M Shechner shechner {- at -} MIT {- dot -} EDU
Date: 2008-02-04

Next message:
Subject: Re: Question about strange MR solution
From: Pietro Roversi pietro {- dot -} roversi {- at -} PATH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-02-05