Molecule Tutorials - Herong's Tutorial Examples - v1.21, by Dr. Herong Yang
Surface Area of Bonded Atoms
This section provides a tutorial on how to use the 'get_area' command to measure the surface area of two bonded atoms in PyMol.
If you want to measure the surface area of two bonded atoms, you can put them into a selection and run the "get_area" command on the selection.
PyMOL>select ch_bond, id 1+2 Selector: selection "ch_bond" defined with 2 atoms. PyMOL>get_area ch_bond cmd.get_area: 23.429 Angstroms^2.
The result shows that the The surface area of two bonded atoms equals to the sum of surface areas of bonding atoms.
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(15.171 + 8.258) 23.429
This seems to be incorrect. The surface area of two bonded atoms should be smaller than the sum of surface areas of both atoms, because they overlap into each other.
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