Hello, I am relatively new to Chimera (and the user group), but am using it to compare ligand binding pockets for multiple (36) structures of related proteins. My proteins overlay nicely based on alignment, but I am having difficulty with the comparisons of multiple structures at once. First, After overlaying multiple protein (pdb) structures with ligands using MultiAlign based on alignment, how does one easily view only the overlaid ligands? [Note: I have up to 36 structures overlaid, each with 0-2 ligands.] Secondly, can chimera then calculate a solvent-accessible closed surface for the protein cavity surrounding each ligand? Alternatively, I could calculate the cavity first, then overlay based on alignment. The goal is to view the overlaid cavities for visual comparison. Thirdly, can chimera calculate electrostatic charge on amino acids surrounding a binding cavity and reflect that charge onto the closed cavity surface? Can this surface be included in overlay view? Given the number of structures, I would much appreciate any advice on how to make this manageable. If Chimera cannot do the calculations, can it import multiple structures saved by another capable software, then overlay them using MultiAlign (including the surfaces)? I appreciate any help provided. Roberta ******************************** Roberta S. King, Ph.D. Assistant Professor Department of Biomedical and Pharmaceutical Sciences College of Pharmacy University of Rhode Island