"get_extent" - Picked Atom Location

This section provides a tutorial on how to measure the location of a picked atom using the 'get_extent' command in PyMol.

PyMol 4 picked atoms identified as pk1, pk2, pk3 and pk4 selections can also be used to get the location coordinates of any picked atom.

"get_extent" prints the extent of a specified selection in a molecule. If you specify pk1, pk2, pk3, or pk4, it prints the extent of a single picked atom. In this case, the extent becomes a point representing the location of the specified atom.

Examples of "get_extent" commands:

PyMOL># prints the location of a picked atom
PyMOL>edit id 1, id 2
PyMOL>get_extent pk2
 cmd.extent: min: [   0.840,  -1.030,   0.000]
 cmd.extent: max: [   0.840,  -1.030,   0.000]

PyMOL># prints the extent of a pair of atoms
PyMOL>select pair, id 1+2
 Selector: selection "pair" defined with 2 atoms.
PyMOL>get_extent pair
 cmd.extent: min: [  -0.181,  -1.392,  -0.126]
 cmd.extent: max: [   0.840,  -1.030,   0.000]

 PyMOL># prints the extent of the entire molecule
 PyMOL>get_extent
 cmd.extent: min: [  -0.181,  -1.875,  -0.813]
 cmd.extent: max: [   1.529,  -0.347,   0.953]

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