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Hi John,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Tom<br>
<br>
<br>
<span style="white-space: pre;">> Hello,<br>
> <br>
> Is it possible, in Chimera, to select only the internal water<br>
> molecules of a protein structure? I need to find out how many
water<br>
> molecules enter the protein structure from the outside during
a<br>
> molecular dynamics simulation.<br>
> <br>
> Thanks!<br>
> <br>
> John</span><br>
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