Using PyMOL to visualize results

The free, open source molecular graphics program PyMOL (www.pymol.org) can read CEX files and display them (simply use the load command to read the pkx1_select.cex and protein+plptypes.cex files). The following views are of ligands selected per the procedure above as viewed in PyMOL. The second and third are two different poses of the same ligand which both satisfy the selection criteria. The rightmost view for each ligand shows the hydrogen bonding interaction which satisfies the selection. The orange sphere shows the position and size of the pocket occupancy rule. Click on any of the views to see larger versions.

First selected ligand	Spacefilling representation	Ligand showing selected interactions
Second selected ligand	Spacefilling representation	Ligand showing selected interactions
Second ligand (pose 2)	Spacefilling representation	Ligand showing selected interactions