Molecule Tutorials - Herong's Tutorial Examples - v1.26, by Herong Yang
"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
Molecule Names and Identifications
Nucleobase, Nucleoside, Nucleotide, DNA and RNA
►"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 Entire Molecule
"get_position" - Viewing Center
ChEMBL Database - European Molecular Biology Laboratory
PubChem Database - National Library of Medicine
INSDC (International Nucleotide Sequence Database Collaboration)
HGNC (HUGO Gene Nomenclature Committee)