CCL: conversion to xyz

 Sent to CCL by: "LI Daobing" [lidaobing+ccl()gmail.com]
 On 8/22/07, Michel Petitjean ptitjean#itodys.jussieu.fr
 <owner-chemistry^ccl.net> wrote:
 >
 > Sent to CCL by: Michel Petitjean [ptitjean(-)itodys.jussieu.fr]
 > To: chemistry_+_ccl.net
 > Subject: CCL: Re: conversion to xyz
 >
 > Look at "multidimensional scaling" with google: it is the
 algorithm
 > converting a n*n distance matrix (well, the matrix is symmetric and
 > its diagonal elements are null) into a n*d matrix of cartesian
 > coordinates, assuming that the distances are measured in the
 > d-dimensional euclidean space.
 > Here you have to set d=3.
 > For those who are interested to use the method with distances
 > issued from a connex molecular graph, note that the multidimensional
 > scaling needs euclidean distances. Adding a constant to the
 > distances (as recommended in some books when the distance
 > is not euclidean) permits to run the algorithm, but the
 > coordinates generated for molecular graphs after projection
 > in a 3D space give a rather poor result.
 >
 > Michel Petitjean,                     Email: petitjean_+_itodys.jussieu.fr
 > ITODYS (CNRS, UMR 7086)
 > 1 rue Guy de la Brosse                Phone: +33 (0)1 44 27 48 57
 > 75005 Paris, France.                  FAX  : +33 (0)1 44 27 68 14
 > http://petitjeanmichel.free.fr/itoweb.petitjean.shape.html
 >
 > Sent to CCL by: "Jon  Lyon" [jtl3z*_*virginia.edu]
 > > Does anyone know of a program (or have a script) to convert the atomic
 distances of a molecule to an xyz file (or z-matrix)?
 > >
 In a common case(for example, data from NMR), the full matrix of
 distance is not available. under this case, you should consider
 distance geometry, there is a small review in the book of A.R.
 Leach(Molecular Modelling, Principles and Applications, 2nd Ed., A. R.
 Leach, 2001, Section 9.5)
 I also remember concoord[1] can deal with this problem, but I am not sure.
 [1] http://www.mpibpc.gwdg.de/groups/de_groot/concoord/
 --
 LI Daobing