[Jmol-developers] Formal charges in pdb files

[Richard Spinney]

I am generating some animations of various organic chemical reactions and am using a multiple model pdb file for the animation. The animation works fine, but I would also like to display the formal charges on the important atoms in the reaction. This works fine for one of the examples (http://undergrad-ed.chemistry.ohio-state.edu/reactions/sn2-ol.html) but fails to display the charge properly in two others (http://undergrad-ed.chemistry.ohio-state.edu/reactions/alkene-br2.html the Br which attaches to the alkene should have a +1 charge, and in http://undergrad-ed.chemistry.ohio-state.edu/reactions/sn1.html the C atom should have a +1 charge when the Cl leaves). I have tried using various formats for the positive charge (i.e. +1, 1+ or 1) but none of them seem to work. Any ideas on would is wrong? (All of the data files are in http://undergrad-ed.chemistry.ohio-state.edu/reactions/)   Thanks, Rick   Richard Spinney Dept of Chemistry Ohio State University 100 West 18th Ave Columbus OH 43210 email: [EMAIL PROTECTED] Phone: (614) 247-6847 Office: MP0008