[Chimera-users] Internal water molecules

Tom Goddard goddard at sonic.net
Tue Mar 8 11:15:27 PST 2011

Hi John,

   Here's an idea about how to define internal water molecules and 
identify them in Chimera.  Make a density map of the molecule at some 
resolution, say 5 Angstroms, using the Chimera "molmap" command, then 
define internal waters to be the ones that are located at a point above 
a certain density threshold.  You can use the Chimera "Values at Atom 
Positions" dialog (menu Tools / Volume Data) to get the interpolated 
density map value at each atom position.  It assigns the density value 
to each atom.  Then you can use the Render by Attribute dialog (menu 
Tools / Structure Analysis) to select just those atoms with values above 
the threshold density.  Then you can intersect that list of atoms with 
waters since it will also include protein atoms.

   All this is easy to do but since you want to do it for many frames of 
a molecular dynamics simulation you need a script that can be run for 
each MD frame.  Unfortunately the values at atom positions and the 
render by attribute selection capability don't have Chimera command 
equivalents.  But those capabilities (like all Chimera capabilities) can 
be used with a Python script.  I could provide you a script if this 
sounds useful.  Also I'll add to our feature request list the need for 
Chimera commands that would allow you to do it without resorting  to Python.


>  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.
>  Thanks!
>  John
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