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
