I wish to use pymol to display pharmacophores. A pharmacophore will basically be a set of points/spheres each colored to represent the atom type it represents (eg hydrophobe, neg charged atom, hydrogen bond donor...).


I have been using compiled graphics objects to display the pharmacophores, however, it would probably be more flexible to use a ChemPy object to represent the pharmacophore. The pharmacophore would be analogous to a molecule and would contain dummy atoms (eg hydrophobe atom, pos charged atom...) instead of the usual atom types. Would this be difficult? Does anyone have documentation on ChemPy?


Also, could someone point me to an example python script to make a simple ChemPy molecule and load it with cmd.load_model()?


Thanks for you help


Michael Sorich

PhD Student

School of Pharmaceutical, Molecular and Biomedical Sciences

University of South Australia

Email: michael.sorich@postgrads.unisa.edu.au



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