• Description
• Contents of this repository
  • Sources
  • Assets
• Installation for Windows OS
  • Source code
• References and useful links
• Acknowledgements

PyMOL-open-source-setup is an open project which provides an easy-to-use installation setup for the open-source version of PyMOL. PyMOL(tm) is a software tool for visualizing and analyzing molecular structures such as proteins, nucleic acids, and small molecules in 3D. PyMOL is a trademark of Schrodinger, LLC. This repository focuses on simplifying the setup process for open-source PyMOL on the Windows operating system. The installation process does not involve the manual configuration of a Python/conda environment, thus facilitating a rapid and straightforward installation. This allows a broader audience to start using the open-source version of PyMOL for research, teaching, or personal use.

The provided files and setup are unofficial (meaning: informal, no warranty, no liability, provided "as is", no connection to Schrodinger LLC).

There are two different languages used in this repository for the setup functionality.

• c_sharp

  • PostInstallationRunner directory: Contains the core files for post-installation processing.
    • Components directory: Contains the PyMolComponent.cs file.
    • Util directory: Contains utility functions relevant for the PyMolComponent.
    • Program.cs file: Contains the main method of PostInstallationRunner.
  • c_sharp.sln file: Solution file for setting up and configuring the development environment.

• inno_setup

  • LICENSE.txt file: Contains the license information for PyMOL and this repository.
  • setup.iss file: Script file used for the installation setup of the PyMOL-open-source-setup.

There are two different directories used for images.

• assets directory
  • convert_to_ico directory: Contains a batch script, which converts the logo.png image into various resolutions (from 16x16 to 256x256) PNG files and a multi-resolution ICO file. Moreover, the directory includes individual PNG files for each resolution, a generated logo.ico file, and the original logo.png.
  • raw directory: Includes the logo in its original vector format as an SVG file.
  • wiki_images directory: Contains images for wiki.

PyMOL-open-source-setup is tested and available for Windows 10 and 11. To be able to run PyMOL, the Microsoft Visual C++ Redistributable packages for Visual Studio 2022 are required. The installation of these packages can be carried out during the installation process, when prompted by the setup.

For a convenient and user-friendly installation click here.

To modify the source code, download or clone the repository. The Inno Setup script may then be altered by opening the relevant file, setup.iss, in a text editor of your choice. The PostInstallationRunner C# project may also be edited by opening the corresponding solution in an appropriate IDE (e.g. Rider/Visual Studio).

PyMOL

• Open-source GitHub repository
• Incentive PyMOL
• Open-source Windows Python wheelfiles

Developer:

• Hannah Kullik

End-user tester:

• Martin Urban

I would like to thank the communities behind the open software libraries, Christoph Gohlke for the wheel files to make the PyMOL installation comfortable (and without the hassle of compling PyMOL from source), Martin Urban for end-user testing and especially Warren L. DeLano for their amazing work.