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 seletion 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".

Distance between Two Atoms in PyMol
Distance between Two Atoms in PyMol

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