Xplor_NOESY_algorithm

[Alexandre Bonvin]

> Does someone know which is the algorith used by Xplor for the 

> calculation of distances from NOESY cross peaks intensities and 

> viceversa? I know the basic (intensity=constant times 1/distance**6) but 

> I do not find in the manual the exact algoritm used in the executable. 

> Could you help me?
> Thanks
> Piero
> 

There isn't any hard coded algorithm to calculate distances from experimental  
NOE intensities in X-PLOR 3.1. Greg Warren here has developped a  
quasi-relaxation matrix refinement method to correct initial (typically  
qualitative) distance restraints based on the difference between calculated and  
experimental NOE data. This will be part of a new X-PLOR release.

For the other way around, from 3D structure to NOE intensities, X-PLOR makes  
use of the standard relaxation matrix theory. The X-PLOR manual (chapter 21)  
and the references therein give a description of the underlying theory. There  
is two ways of calculating NOE intensities in X-PLOR: a) by diagonalisation of  
the complete relaxation matrix b) by using a spherical cutoff around each  
proton pair.

Alexandre

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| Alexandre Bonvin PhD           | Phone: (203) 432-5066                 |
| Mol. Biophys. & Biochemistry   | Fax:   (203) 432-3923                 |
| Yale University                | Email: abonvin at laplace.csb.yale.edu   |
| New Haven CT 06520-8114, USA   | http://xplor.csb.yale.edu             |
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