Hi John,
Please see the previous reply to a similar question:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-August/005459.html>

To summarize, the "Find Clashes/Contacts" tool identifies contacts of all types and "FindHBond" identifies hydrogen bonds.  There are various choices of what to do with the identified contacts, such as selecting them or writing out all the information to a file.  Selections can be further acted upon (for example, their residue labels shown) using the Actions menu.   See the previous reply for links to the relevant manual pages. 

Examples of use are included in the "Structure Analysis and Comparison" tutorial:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>

Best,
Elaine
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Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 29, 2010, at 12:10 PM, Beale, John wrote:

I am working with a protein in explicit water. Using AMBER tools, I have selected the 100 closest water molecules in and around the protein. Is there a way in Chimera to identify which amino acid residues that the waters are hydrogen bonded to? Or, is there a way to visualize which amino acids the water molecules are closest to?