From: Yarrow Madrona (
Date: Sat Apr 06 2013 - 20:46:00 CDT


Does anyone know how to visualize water movement over the course of a

I know how to select waters within a distance for a given frame. However
since they are entering and leaving the index numbers will change. I can
write out all of the PDBs and read them back in but I am wondering if
there is some script out there that will follow only waters that show up
within a distance of the active site regardless of the index number.

For example water "1" leaves and 20 frames later water "200" enters within
5 angstroms of a FE atom. I want to be able to visualize the water 1 while
it is within 5 angstroms and the water 200 while it is within 5 angstroms
but not when they are greater than 5 angstroms. Thank you for any help you
can provide.

Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697