Aug 20, 2010

Calculate Volume

Quick: what is the volume of this molecular suface?

Here I present a simple method for calculating the volume of a geometric object in PMV.
1. Open Vision.
2. Load the Visualization Library.

3. Drag down the 'PolyhedronVolumeArea' node from the mapper menu and the 'Choose Geom' node from the filter menu in the Visualization library. Drag down the 'PMV Viewer' node in the PMV library. Drag down the 'PopUpMsg' from the Standard Library.
4. Arrange them: PMV Viewer to Choose Geom to PolyVolArea to PopUpMSG. See picture below:
Be sure to choose the geometry you'd like to calculate the volume for.
Here, I have chosen the molecular surface.


5. The volume will appear in the Python IDLE Shell.
Note: units are in Angstroms.

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