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

_______________________________________________
Chimera-users mailing list
Chimera-users@cgl.ucsf.edu
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users