Dihedral Angle Formed by 3 Atoms in PyMol

This section provides a tutorial on how to measure the dihedral angle formed by 4 picked atoms using the 'get_dihedral/dihedral' command in PyMol.

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

"get_dihedral" prints the dihedral angle formed by 4 picked atoms in the message output console:

# print dihedral angle formed by 4 atoms: pk1, pk2, pk3, pk4
get_dihedral

# print dihedral angle formed by 4 atoms: pk2, pk3, pk4, pk1
get_dihedral pk2, pk3, pk4, pk1

"dihedral" creates a new visualization seletion to show the dihedral angle formed by 4 picked atoms:

# create dihedral angle (named as dih1) formed by pk1, pk2, pk3, pk4
dihedral dih1

# create dihedral angle (named as ang2) formed by pk2, pk3, pk4, pk1
dihedral dih2, pk2, pk3, pk4, pk1
Dihedral Angle Formed by 4 Atoms in PyMol
Dihedral Angle Formed by 4 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