Xplor_NOESY_algorithm
Alexandre Bonvin
abonvin at LAPLACE.CSB.YALE.EDU
Thu Nov 2 15:58:18 EST 1995
> 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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