On Feb 28, 2011, at 11:44 AM, Beale, John wrote:

Hello,
 
Is it possible, in Chimera, to select only the internal water molecules of a protein structure? I need to find out how many water molecules enter the protein structure from the outside during a molecular dynamics simulation.
 

Hi John,
I pretty sure this requires some (possibly simple) Python scripting.  No script can really be written though without the answer to this question:  what is your definition of "internal"?

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu