Rolf, that example works fine for me. You have the problem that you have a carbonyl on an "aromatic" ring that has heteroatoms. In this case you can't expect Jmol to handle it properly. You have to help it with heteroatoms.
load http://www.fli-leibniz.de/ImgLibPDB/tmp/061.cif script http://www.fli-leibniz.de/ImgLibPDB/tmp/061.jmz select (C33 or O34) connect aromatic modify # add C=O to aromatic set. select (C33 or N19 or C20) connect single modify # remove N19 from aromatic set select (N3,N4,C5) #remove N4 from aromatic set connect single modify calculate aromatic moveto /* time, axisAngle */ 1.0 { 996 -86 35 93.47} /* zoom, translation */ 102.94 0.0 0.0 /* center, rotationRadius */ {0.6127415 0.09991381 0.14189662} 9.57882 /* navigation center, translation, depth */ {0.0 0.0 0.0} -3.1372375 -0.9668884 50.0; That should look terrific. It's possible that the algorithm could be adapted to include N atom aromaticity. That could actually be very interesting. I think it might work for the tetrazole. I wonder if the simple rule that N with two aromatic singles and no double would be OK provided the valency is 3. Might work.... Of course protonated amines obey a C rule.... Bob Rolf Huehne wrote: > >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 > > -- 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
