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Dear
CCL'ers,
My original enquiery was : I am looking for a program
to animate MD trajectories, with polyhedral
representation of crystal structures. I shall be grateful for any suggections, and summarise them. Also, does anyone know what is the Web-site of Babel? Many thanks to Keith Refson, Robert Best and Ricardo Grau Crespo, whose replies (slightly shortened) I summarise below: Keith Refson :
Cerius 2 does this I think. But perhaps you
are looking for something
free. You probably need the MD modules as well as the crystal builder. AVS : there's Larry Finger's "crystal" AVS module which can be used for polyhedral representations. And you can use AVS to animate. However it has it's own unique structure format files. On a Win32 PC there's MSI's free WebLab viewer which I believe will do this. I'm not aware of anything free for unix which does. Babel is pretty useless at converting between periodic crystal structure files and usually loses all symmetry and unit cell information. I have written some perl scripts for converting between PDB/Schakal and CASTEP formats if you are interested. They are in ftp://ftp.earth.ox.ac.uk/pub/keith/cteptouts.tar.gz Robert Best :
A good program for displaying trajectories and
doing analysis is gopenmol,
available from http://laaksonen.csc.fi/gopenmol. Although the emphasis is on analysis of amorphous systems, there is a facility for drawing cubic cells, and you can draw any kind of cell using the built-in tcl scripting. Of course there are crystallographic programs which make the cell drawing easier, but I don't know of any that have the ability to display trajectories as well. Ricardo Grau Crespo :
Babel lives in a lot of places on the net,
but the "official" distribution site is http://www.eyesopen.com/babel.html **********************************************************************
Artem R. Oganov, Doctorate Student in Crystallography and Mineral Physics, Dept. of Geological Sciences, University College London, Gower Street, London WC1E 6BT, U.K. E-mail : a.oganov ( ( at ) ) ucl.ac.uk Tel. : +44 (0)171-419-3449 Fax : +44 (0)171-387-1612 **********************************************************************
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