[Chimera-users] Internal water molecules

Tom Goddard goddard at sonic.net
Tue Mar 8 16:14:09 PST 2011

Hi John,

   I just added a Chimera command to get density map values at atom 

     measure mapValues #0 #1:HOH name pdensity

Here the map is #0 and it assigns an atom attribute named "pdensity.  
Eric Pettersen points out that you can select atoms based on attribute 
values using an atom specifier like

     select #1@/pdensity>.05

The measure mapValues command will be in tonight's Chimera daily builds.


> 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.
>     Tom
> > 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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