Angle Formed by 3 Atoms in PyMol

This section provides a tutorial on how to measure the angle formed by three picked atoms using the 'get_angle/angle' command in PyMol.

PyMol 4 picked atoms identified as pk1, pk2, pk3 and pk4 selections can also be used to measure the angle formed by 3 atoms.

"get_angle" prints the angle formed by three picked atoms in the message output console:

# print angle formed by 3 atoms identified by pk1, pk2, pk3
get_angle

# print angle formed by 3 atoms identified by pk2, pk3, pk4
get_angle pk2, pk3, pk4

"angle" creates a new visualization selection to show the angle formed by three picked atoms:

# create angle (named as ang1) formed by pk1, pk2, pk3
angle ang1

# create angle (named as ang2) formed by pk2, pk3, pk4
angle ang2, pk2, pk3, pk4
Angle Formed by 3 Atoms in PyMol
Angle Formed by 3 Atoms in PyMol

Table of Contents

 About This Book

 Introduction of Molecules

 Molecule Names and Identifications

 Molecule Mass and Weight

 Protein and Amino Acid

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

 DNA Sequencing

 Gene Mutation

 SDF (Structure Data File)

 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)

 HGNC (HUGO Gene Nomenclature Committee)

 Relocated Tutorials

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB