From owner-chemistry@ccl.net Tue Aug 21 18:11:01 2007 From: "LI Daobing lidaobing+ccl|-|gmail.com" To: CCL Subject: CCL: conversion to xyz Message-Id: <-34971-070821180911-17783-wFg8JQggROeJHogp6+mtQA.:.server.ccl.net> X-Original-From: "LI Daobing" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 22 Aug 2007 06:08:49 +0800 MIME-Version: 1.0 Sent to CCL by: "LI Daobing" [lidaobing+ccl()gmail.com] On 8/22/07, Michel Petitjean ptitjean#itodys.jussieu.fr 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