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.

Table of Contents

 About This Book

 Introduction of Molecules

 Molecule Names and Identifications

 Protein and Amino Acid

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

 SDF (Structure Data File)

 RDKit: Open-Source Cheminformatics Software

 PyMol Installation

 PyMol GUI and CLI

 PyMol Selections

 PyMol Editing Functions

PyMol Measurement Functions

 "get_extent" - Picked Atom Location

 "label" - Generate Labels on Atoms

 Distance between Atoms in PyMol

 Angle Formed by 3 Atoms in PyMol

 Dihedral Angle Formed by 3 Atoms in PyMol

 Use Selection Expressions in PyMol

 "get_area" - Surface Areas of Atoms

Surface Area of Bonded Atoms

 Surface Area of Entire Molecule

 "get_position" - Viewing Center

 PyMol Movie Functions

 PyMol Python Integration

 PyMol Object Functions

 ChEMBL Database - European Molecular Biology Laboratory

 PubChem Database - National Library of Medicine

 PDB (Protein Data Bank)

 INSDC (International Nucleotide Sequence Database Collaboration)

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB