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 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. -Tom ----- Original Message ----- From: "Miguel Howard" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Cc: <[EMAIL PROTECTED]> Sent: Friday, December 12, 2003 12:07 PM Subject: Re: [Jmol-users] aromatic bonds > Tom, > > Thanks for the .mol file that contains aromatic bonds. > > > At the bottom of the .mol file you will see a > > listing like this. > > The first two colomns are the atom numbers. The third column is the bond > > order: 1 for single, 2 for double, 3 for triple, 4 for aromatic. > > > > This .mol file was created by gaussview 03. > > ================================.mol file excerpt > > ========================================= > > > > cyclopentadiene and aryl oxide titanium cation with benzene adsorbed > > > > Created by GaussView 3.07 > > 39 39 0 0 0 0 0 0 0 0 0 > > --> There are 39 atoms > > 0.0000 0.0000 0.0000 Ti 0 0 0 0 0 0 0 0 0 0 0 > > --> This section lists the x, y, z coords and atomic symbol > > 2.0390 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 > > --> (I have no idea what the 0's are for) > > 2.3940 1.0376 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > > 2.4349 -0.5063 0.8851 H 0 0 0 0 0 0 0 0 0 0 0 0 > > 2.3945 -0.5254 -0.8945 H 0 0 0 0 0 0 0 0 0 0 0 0 > > 25 27 1 0 0 0 > > --> This lists the bond information: first atom, second atom, bond > > order > > 28 29 1 0 0 0 0 > > 29 30 4 0 0 0 0 > > 29 31 4 0 0 0 0 > > 30 32 4 0 0 0 0 > > 30 33 1 0 0 0 0 > > 31 34 4 0 0 0 0 > > 31 35 1 0 0 0 0 > > 32 36 4 0 0 0 0 > > > One of the problems I have been thinking about with aromatic bonds is the > way to render them. > > I would like to do it as a solid cylinder and a segmented/dotted cylinder, > with the segmented cylinder on the 'inside' of the ring. > > I have been thinking that the easy way to tell the 'inside' of the ring is > to find an adjoining atom which has an aromatic bond and looking at the > direction of the atom at the other end of that bond. > > Does that make sense? > > (Sorry if I didn't describe it very well :-) > > > I would also like to point out another molecule format which appears to > > be very versatile and easy to understant. The .mol2 (or .ml2) file type > > which indicates the aromatic bond by Ar. > > I will look into the mol2 file format. > > > 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
