Miguel, > Hens, what computation package are you using to generate your files? > Most of the time I use MOPAC and its options to scan a coordinate (distance, dihedral angle). Then I read the output into MOLDEN (not only because I share the office with its author) that will write out an m-XYZ file. With Gaussian the same path is followed.
(B.t.w. we also have a MOPAC web interface that will do the same directly, all perl that extracts the structures and writes the m-xyz format, creates a web page with the animation, control buttons etc.) MOLDEN does write the m-XYZ for vibrations as well. About the bonding information in an animation: the point is that it can change from frame to frame. Think of the Diels-Alder reaction, where bonds move from none to single, single to double and vice versa. That's what I had in mind when I wrote 'editing by hand'. Complicated but not impossible to be handled by a script, provided you feed it with accurate distance criteria. Although you (Miguel) wrote that JMol is not a bonding tool: Personally I'd like see the gradual change, say from single to double, by splitting the bond, or playing with the transparency. We tried this in Java3D and it worked. Hens ------------------------------------------------------- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps & Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
