What Is PyMol
This section provides a quick introduction of PyMol, a powerful molecule visualization software.
PyMol is a powerful molecule visualization software with the following main features:
- Able to produce high-quality graphics ready for publications.
- Able to create movies.
- Able to measure bond distances and angles.
- Has an extensive help system.
- Structures can be sliced, diced, and reassembled on the fly and written out to
- Both command line interface and graphical user interface are provided.
- Python API is provided to access all functionalities.
PyMol was originally written by Warran Delano in Python in the
early 2000's and released as an open-source project.
Unfortunately, Warren passed away in 2009. PyMol is maintained now by
Schrodinger with 2 editions: free academic edition and commercial edition.
For more information, visit PyMol Website at
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
►What Is PyMol
Install PyMol Incentive Edition on macOS
Install PyMol Open Source Edition
Compile PyMol Source Code
Install Open Source PyMol with Homedrew
Install Open Source PyMol with Fink
PyMol GUI and CLI
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
Full Version in PDF/EPUB