• 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.

• 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 will be carried out during the installation process.

For a convenient and user-friendly installation click here.

Install location: C:\Users\<Username>\AppData\Roaming\PyMOL-Open-Source\bin

Paste the following path in your Windows explorer:

%USERPROFILE%\AppData\Roaming\PyMOL-Open-Source\bin

In addition to the one-click installer, a portable ZIP package is available for the PyMOL application. This package is particularly useful for scenarios where the one-click installer may not function as expected.

The portable ZIP file includes the necessary Microsoft Visual C++ Redistributable packages for Visual Studio 2022. However, for the application to run correctly, the Microsoft Visual C++ Redistributable packages for Visual Studio 2022 must be installed on the system. These packages can either be pre-installed on your system or installed using the bundled package included in the ZIP file.

• Python
  • Minimum: Python 3.10
• Inno Setup compiler version 6
  • Installed in C:\Program Files (x86)\Inno Setup 6\ISCC.exe!

• MSBuild
  • Part of VS 2022 (incl. Community edition)
• CMake
  • To download the MSI installer click here
  • To download the portable version click here
  • Be aware: Add the cmake.exe to your PATH variable (short guide). Check by running cmake --version

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.

To reproduce the setup and portable ZIP file, use the run_automation.bat file with the following commands:

1. Create Python virtual environment

.\run_automation.bat init

2. Setup build environment

.\run_automation.bat setup-dev-env

3. Compile inno setup to setup.exe

.\run_automation.bat build-setup-exe

4. Optional: Create a ZIP file containing a standalone (portable) application

.\run_automation.bat build-portable

PyMOL

• Open-source GitHub repository
• Incentive PyMOL
• Unofficial PyMOL Windows Build (Binary Wheel)

Developer:

• Hannah Kullik

End-user tester:

• Martin Urban

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