From: Marc Zimmer (
Date: Sat Aug 07 2010 - 19:51:26 CDT


We have a trajectory of our protein in a box of waters and would like to
superimpose the protein and plot the position of a specific water molecule
in each frame, so that we can get an average protein structure (or a
representative protein structure) with position of the water molecule in all
the frames superimposed on that single protein structure showing the
pathway that water takes out of the protein.

Any suggestions or scripts would greatly be appreciated.

Thanks a lot

Marc Zimmer