What Is PyMol

Molecule Tutorials - Herong's Tutorial Examples

∟PyMol Installation

∟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 standard files.
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 pymol.org.

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)

SDF (Structure Data File)

►PyMol Installation

►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 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)

HGNC (HUGO Gene Nomenclature Committee)

Relocated Tutorials

Resources and Tools

Molecule Related Terminologies

Full Version in PDF/EPUB