Bob Hanson wrote: > 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 >
Thanks Bob! Since 11.3.29 is not released yet I checked out the latest version from SVN an hour ago and tried it out. I used the same example as before (http://www.fli-leibniz.de/ImgLibPDB/tmp/061.cif , http://www.fli-leibniz.de/ImgLibPDB/tmp/061.jmz). After loading the script I issued the following commands: smartAromatic=true; reset aromatic; calculate aromatic; Afterwards all aromatic bonds were shown as double bonds with 2 solid lines. I think I usually will prefer this representation, combined with a different color for aromatic and double bonds. But as far as I understood it should now also be possible to get alternating single and double bonds. So I also tried to set the first bond to "aromaticSingle" or "aromaticDouble": reset aromatic; connect (atomno=1) (atomno=2) aromaticSingle; calculate aromatic; But in both cases there was no difference: all aromatic bonds were double bonds. Regards, Rolf ------------------------------------------------------------------------- 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
