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In this project the student will extend Jmol with the ability to view pharmacophores. The pharmacophore is a concept of ligand binding where a set of three or more spheres (other versions have been defined too, but this is the starting point) define what a molecule should look like to fit well into the protein cavity. The spheres indicate areas where proton donors/acceptors or other features should be, and the pharmacophore defines the intersphere distances.


  • add ability to contain pharmacophores in the data model
  • add a scripting command to define such spheres
  • add ability to draw (transparent) spheres at arbitrary place with arbitrary radius