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From: Yarrow Madrona (amadrona_at_uci.edu)
Date: Sat Apr 06 2013 - 20:46:00 CDT
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Hello,
Does anyone know how to visualize water movement over the course of a
trajectory?
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
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