Re: [ccp4bb]: How to evaluate local coordinate error (?)

[Yu Wai Chen <ywc@mrc-lmb.cam.ac.uk>]

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> We are presently working on the structure of a mutant wherein this mutant
> appears to have the rigid body movement of a 15 residue alpha-helix by
> about 1 Angstrom relative to the position of the helix in the wild-type.
> This movement is "detected" by the 2.5 sigma density of a simulated
> annealing fofc omit map. The problem is that our reflection data is 2
> sigma only to about 3.2 Angstroms. So my questions are: How valid are any
> conclusions derived from this perceived movement?

2.5 sigma seems to be a bit low for fofc map.  A lot of noises show up at 
this level.

If your density is genuine, the overall coordinate error can be estimated 
by the Luzzati plot of R-factors and Rfree.  Also if you run refmac, it 
gives you an estimate based on maximum liklihood.  For local fitness, you 
can calculate real-space correlation coefficient with O.  You can compare 
the Rfree before and after you moved your rigid-body.  If you do not see an 
Rfree dropping, you are fitting the model to noise.

Wai
===================================================================
Yu Wai CHEN, Ph.D. ..................   email:ywc@mrc-lmb.cam.ac.uk
 Centre for Protein Engineering,             tel:+44-(0)1223-402148
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