Well, guess what? I think I figured it out. version=11.3.29 (Nico -- this is ready for release)
# new feature: aromaticSingle and aromaticDouble bond order options # new feature: select ISAROMATIC # selects aromatic atoms bonds that look like single and double bonds can still be considered aromatic, and atoms connected by such bonds can be selected using ISAROMATIC. (AROMATIC itself is a RasMol reserved keyword). # new feature: "smartaromatic" bonds # turned off with "smartAromatic = false" # new feature: calculate aromatic # calculates reasonable aromatic double/single alternation. # new feature: reset aromatic # sets all aromaticDouble and aromaticSingle back to aromatic Jmol will now calculate alternating aromatic bonds. This should go a long way to improving the look of aromatic rings. You can turn this feature off using smartAromatic = false And you can specify the alternation by indicating any one bond's state and then recalculating reset aromatic connect (atomno=9) (atomno=12) aromaticDouble calculate aromatic # new feature: MOL reader recognizes bond types 4,6,7 4 is loaded as aromatic 6 and 7 are loaded as aromaticSingle and aromaticDouble Bob Angel Herraez wrote: >El 4 Oct 2007 a las 7:41, Bob Hanson escribió: > > >>I'll look into this. But it is a VERY difficult problem, actually. >> >> > >In fact, I thought it was impossible, and had given up on it until >Bob posted yesterday about negative signs. > >I agree with Rolf, but the "inner" location is only clear with single >rings. Take for ex. purine and you are bound to have trouible >deciding which is the inner side of the shared bond. Not to mention >more complex polycyclic molecules! > > > I looked at the algorithm. It's very simplistic -- find the >------------------------------------------------------------------------- >This SF.net email is sponsored by: Splunk Inc. >Still grepping through log files to find problems? Stop. >Now Search log events and configuration files using AJAX and a browser. >Download your FREE copy of Splunk now >> http://get.splunk.com/ >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
