[Chimera-users] viewing & comparison of multiple overlay structures

Roberta King rking at uri.edu
Tue Apr 3 13:47:49 PDT 2007



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 S. King, Ph.D.

Assistant Professor

Department of Biomedical and Pharmaceutical Sciences

College of Pharmacy

University of Rhode Island



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