Bob put this together in 2006. I think you'll find it useful if you use Angel's connected() suggestion:
http://chemapps.stolaf.edu/jmol/docs/misc/groups.txt Otis -- Otis Rothenberger [email protected] http://chemagic.com On Jun 24, 2013, at 9:42 AM, Angel Herráez wrote: > Hello Gudrun > >> Jmol seems to have a feature that allows functional groups to be >> highlighted. > > Yes. You can use either connected() commands or the SMARTS > expressions in your script. > > >> Could you advise me how and where to introduce the highlight functional >> groups function into my source so that I can choose a colour that >> highlights the functional group(s) in my molecules? > > Normally you would do > > 1. define your target atom set (using connected or smarts) > 2. select it > 3. apply a highlight, e.g. color, halos, size... > 4. unselect (not essential but a good practice) > > All that may go inside the page in the form of JavaScript or maybe > JmolScript inside the javascript > Regarding the choice of a color, either you hard-code it or it is > purely a question of html interface (e.g. a drop-dwon menu for the > user to pick) > > See > > http://chemapps.stolaf.edu/jmol/docs/#jmolsmarts/smiles > > http://chemapps.stolaf.edu/jmol/docs/#atomexpressions and then > Functions > CONNECTED() > > http://wiki.jmol.org/index.php/Recycling_Corner#Molecule_color_picker > > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
