----- Original Message ----- From: Miguel <[EMAIL PROTECTED]> Date: Wednesday, October 29, 2003 9:19 am Subject: Re: [Jmol-users] JmolApplet Wish List
> > Just discovered, downloaded and spent a few hours playing with > > Jmol-8/JmolApplet-8 and the ?sneak preview? of Jmol-10. ABSOLUTELY > > BRILLIANT! > Glad that you like Jmol > > > The materials I have been working on have been mainly targeted at > > pre-university level (AS and A2 level in UK edu-speak) and involve > > inorganic crystal and metal structures as well as organic molecules > > and biopolymers. All currently use .pdb format. > > Phillip Barak of the University of Wisconsin USA recently sent me > a link > that shows some excellent web pages with inorganic molecules. You > shouldtake a look at them: > http://www.soils.wisc.edu/virtual_museum/ Just to jump in here about our use of pdb files for the minerals on our site: Using pdb was not our first choice. We would have prefered CIF format, files with the barest minimum of spatial information, since symmetry operators allow 'tiling' out in any direction per user parameters, but that was not to be with Chime. (WebLab viewer did a nice job of asking how many cells in each direction and then drawing it up.) Then of course, we found that Rasmol/Chime didn't do a very good job of connecting bonds (allowing Si-Si bonds and Si-Al bonds when it should have been Si-O-Si or Si-O-Al.) And Chime never seemed to get the unit cell drawn correctly. For a while, we used mol format, with bonds specified, but the number of atoms was too limited for any but the smallest mineral models. We moved on to pdb files, with positions and bonds specified, and some of these models require relatively large files. This works well but quite a bit of spacially redundant information is included in the pdb or mol file. --Phil Barak ------------------------------------------------------- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
