Compile PyMol Source Code

This section provides a tutorial on how to download PyMol open source edition source code and compile it on macOS. Compilation failed with 'GL/glew.h' file not found.

If you want to install the open source edition of PyMol from source code, you can try these steps:

1. Go to PyMol GitHub repository at

2. Click "Clone or Download > Download ZIP". A ZIP file will be downloaded and unzip in your ~/Download directory.

3. Go to downloaded source directory ~/Download/pymol-open-source-master. And verify source code files.

4. Run the following command to try to compile the code:

herong$ cd ~/Download/pymol-open-source-master
herong$ python install --prefix=~/pymol

running install
running build
running build_py
running build_ext
building 'pymol._cmd' extension
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 ...
c++ -std=c++11 -arch x86_64 -arch i386 -pipe -D_PYMOL_LIBPNG ...
layer0/os_gl.h:68:9: fatal error: 'GL/glew.h' file not found
1 error generated.

Obviously, the compilation process failed. It looks like missing some required package. I will check on this later.

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

 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)

 Resources and Tools

 Molecule Related Terminologies


 Full Version in PDF/EPUB