Molecule Tutorials - Herong's Tutorial Examples - v1.26, by Herong Yang
Distance between Atoms in PyMol
This section provides a tutorial on how to measure the distance between two picked atoms using the 'get_distance/distance' command in PyMol.
PyMol 4 picked atoms identified as pk1, pk2, pk3 and pk4 selections can also be used to measure distances between atoms.
"get_distance" prints the distance between two picked atoms in the message output console:
# print distance between the first two picked atoms get_distance # print distance between picked atoms #3 and #4 get_distance pk3, pk4
"distance" creates a new visualization selection to show the distance between two picked atoms:
# create distance (named as dis1) between the first two picked atoms distance dis1 # create distance (named as dis2) between picked atoms #3 and #4 distance dis1, pk3, pk4
Note that the unit of measure for distance is "angstrom".
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)