Emily, I'm not sure, but check out Eric Martz's work on "FirstGlance 
in Jmol". I seem to remember he implemented sequence selection and 
highlighting:  http://firstglance.jmol.org

If not, maybe somebody else has done it and that's why I remember.
In any case, it's a question of sitting down and implementing; the 
functionality is there in Jmol scripting language.

For once, I'll be daring: it's not in my priority list, but I could 
do it if the stimulus is strong enough:
http://sourceforge.net/services/project_services.php?project_id=23629
:-)




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