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Hi John,<br>
<br>
I just added a Chimera command to get density map values at atom
positions.<br>
<br>
measure mapValues #0 #1:HOH name pdensity<br>
<br>
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<br>
<br>
select #1@/pdensity>.05<br>
<br>
The measure mapValues command will be in tonight's Chimera daily
builds.<br>
<br>
Tom<br>
<br>
<br>
<blockquote cite="mid:4D76804F.7090908@sonic.net" type="cite">
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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>
> <br>
<br>
> Is it possible, in Chimera, to select only the internal
water<br>
<br>
> molecules of a protein structure? I need to find out how
many<br>
water<br>
<br>
> molecules enter the protein structure from the outside
during<br>
a<br>
<br>
> molecular dynamics simulation.<br>
<br>
> <br>
<br>
> Thanks!<br>
<br>
> <br>
<br>
> John</span><br>
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<br>
<br>
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