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
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Roberta S. King, Ph.D.
Assistant Professor
Department of Biomedical and Pharmaceutical Sciences