Molecule Tutorials - Herong's Tutorial Examples - v1.21, by Dr. Herong Yang
Surface Area of Entire Molecule
This section provides a tutorial on how to use the 'get_area' command to measure the surface area of the entire molecule in PyMol.
If you want to measure the surface area of the entire molecule, you can run the "get_area" command without any argument.
PyMOL>get_area cmd.get_area: 47.949 Angstroms^2.
The result shows that the The surface area of the entire molecule is about the same as the sum of surface areas of all atoms in the molecule.
PyMOL>get_area id 1 cmd.get_area: 15.171 Angstroms^2. PyMOL>get_area id 2 cmd.get_area: 8.258 Angstroms^2. PyMOL>print str( 1*15.171 + 4*8.258) 48.202999999999996
This seems to be incorrect. The surface area of the entire molecule should be smaller than the sum of all atoms in the molecule, because they overlap into each other.
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