Hens wrote: > 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.
I am not familiar with any of these tools, but it is helpful for me to have a little understanding of the process. > 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'. Correct. And I think that it is important that this bonding be controlled by the author, or by a better tool than Jmol. > 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. I agree with this 100%. Transparency is currently very difficult for me to work with ... the current graphics engine does not support it. I have been thinking about the frame interpolation when a bond disappears. That is, when the bond is present in one frame but not in another. I was thinking of have the size of the bond reduce to zero during the interpolated frames. I had not thought about the double-to-single bond transition, but I trust that we can come up with something. Miguel > 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
