Molecule Tutorials - Herong's Tutorial Examples

∟PyMol Installation

This chapter provides quick an quick introduction about PyMol, a powerful molecule visualization software. Installation tutorials are also provided.

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

Takeaways:

• PyMol is a powerful open-source molecule visualization software.
• PyMol has two editions: Incentive Edition for paying sponsors, and Open Source Edition for free.
• Installing PyMol Incentive edition is straightforward.
• Installing PyMol Open Source edition is very challenging.

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)

 DNA Sequencing

 Gene Mutation

 SDF (Structure Data File)

►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)

 HGNC (HUGO Gene Nomenclature Committee)

 Relocated Tutorials

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB

PyMol Installation - Updated in 2023, by Herong Yang