[Chimera-users] Internal water molecules
goddard at sonic.net
Tue Mar 8 11:15:27 PST 2011
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.
> 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.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Chimera-users