can someone please suggest a good example mol file to show aromatic bonds? thanks!
:tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest at 11.06a EDT on 2003 December 17 Wednesday Miguel Howard said: > > Yes, I think your idea will work. All aromatic bonds have to have > > adjacent aromatic bonds. So if you find an adjacent aromatic bond, > > that should tell you the inside of the ring. > > The code for rendering aromatic bonds in Jmol implemented and checked > into CVS. > > It correctly detects the inside of the ring. > > Note that this is only rendering the bonds as 'aromatic' if the file > contents indicate that it is an aromatic bond. The only file type that > supports this currently is .mol > > The outstanding issues are: - the inside (dashed) lines are a bit too > long. As with other bonds, they run to the center of the atom. This > means that they actually overlap by a few pixels. Doesn't look very > good. The inside/dashed line needs to be shortened a bit. > > - The cylinder representation of a dashed line is ugly. I did it as a > series of spheres, but it needs to be a broken/dashed cylinder. > > > The only problem you might run into is if you have two adjacent > > aromatic rings how can the bond common to the two rings be rendered? > > Then you might want to consider placing a dashed line on both sides > > of the bond. > > In the situation where an aromatic bond participates in more than one > ring: - the 'inside' will be determined based upon the first ring that > is encountered - there is (effectively) no way to control which ring it > is associated with - it *will* be consistent, in that it will not > change from one ring to another while the molecular model is rotated. > > > Miguel > > > > > > > ------------------------------------------------------- This SF.net > email is sponsored by: IBM Linux Tutorials. Become an expert in LINUX > or just sharpen your skills. Sign up for IBM's Free Linux Tutorials. > Learn everything from the bash shell to sys admin. Click now! > http://ads.osdn.com/?ad_id=1278&alloc_id=3371&op=click > _______________________________________________ Jmol-users mailing list > [EMAIL PROTECTED] > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------- This SF.net email is sponsored by: IBM Linux Tutorials. Become an expert in LINUX or just sharpen your skills. Sign up for IBM's Free Linux Tutorials. Learn everything from the bash shell to sys admin. Click now! http://ads.osdn.com/?ad_id=1278&alloc_id=3371&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
