PyMol Measurement Functions

This chapter provides quick introductions on using PyMol to access measurements and properties of substructures or the entire molecule in PyMol.

"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

Takeaways:

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

 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