Use Selection Expressions in PyMol

This section provides a tutorial on how to use atom selection expressions in measurement commands directly, instead of pk1, pk2, pk3 and pk4 selection names in PyMol.

PyMol commands supports selection expressions directly, in addition to selection names or default selections.

For example, the following commands creates new measurement selections with atom selection expressions:

# create distance between atom #2 and #3
distance dis1, id 2, id 3

# create angle formed by atom #3, #4 and #5
angle ang1, id 3, id 4, id 5

# create dihedral angle formed by atom #3, #1, #4 and #5
dihedral dih1, id 3, id 1, id 4, id 5

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