{"id":26477675,"url":"https://github.com/urban233/pymol-open-source-linux-build","last_synced_at":"2026-04-24T22:33:58.506Z","repository":{"id":281647327,"uuid":"945932740","full_name":"urban233/pymol-open-source-linux-build","owner":"urban233","description":"Unofficial binary wheels for the open-source version of PyMOL, (including an updated menu stylesheet and an alternative splash screen) tailored for Python on GNU 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unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["linux","open-source","pymol","python-wheel"],"created_at":"2025-03-20T00:48:06.770Z","updated_at":"2026-04-24T22:33:58.492Z","avatar_url":"https://github.com/urban233.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Unofficial PyMOL GNU Linux Build (Binary Wheel)\n[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-blue.svg)](https://GitHub.com/urban233/pymol-open-source-linux-build/graphs/commit-activity)\n[![GitHub issues](https://img.shields.io/github/issues/urban233/pymol-open-source-linux-build)](https://GitHub.com/urban233/pymol-open-source-linux-build/issues/)\n[![GitHub contributors](https://img.shields.io/github/contributors/urban233/pymol-open-source-linux-build.svg)](https://GitHub.com/urban233/pymol-open-source-linux-build/graphs/contributors/)\n\nThis repository offers **unofficial** binary wheels for the open-source version of PyMOL.\n\n## Contents of this document\n* [About PyMOL](#About-PyMOL)\n* [Contents of this repository](#Contents-of-this-repository)\n  * [Sources](#Sources)\n  * [Documentation](#Documentation)\n  * [Assets](#Assets)\n* [Build](#Build)\n  * [Wheel file](#Wheel-file)\n    * [Pre-built _cmd module](#Pre-built-_cmd-module)\n    * [Self built _cmd module](#Self-built-_cmd-module)\n  * [From source](#From-source)\n    * [Prerequisites](#Prerequisites)\n    * [Step-by-step guide](#Step-by-step-guide)\n* [Roadmap](#Roadmap)\n* [Acknowledgements](#Acknowledgements)\n\u003c!--* [References and useful links](#References-and-useful-links) --\u003e\n\n## About PyMOL\n[PyMOL™](https://pymol.org/) is a powerful visualization software for rendering and animating 3D molecular structures. PyMOL is a trademark of Schrödinger, LLC.\n\nPlease note that the files provided here are **unofficial**. They are informal, unrecognized, and unsupported, offered for testing and evaluation purposes only. No warranty or liability is provided, and the software is made available \"as-is.\"\n\n## Contents of this repository\n### Sources\nAll PyMOL sources are directly from the pymol-open-source GitHub repository\nand are only cloned during the setup process. A stable version is also \nchecked out to avoid build failures due to development code.\n\n### Scripts\nThere are two Python scripts that are used for building PyMOL specific\nshader files and for freezing the Python environment using cx_freeze.\n\n### Pre-built\nTo enable the direct build of a ready-to-use wheel file, a pre-built\n`_cmd` module is already compiled and will be used in the wheel build process\nif no self built one can be found.\nFurthermore, the libGL library is also provided to make the build process\neasier and less error-prone.\n\n### Vcpkg\nTo make the build process of the `_cmd` module as easy and convenient as \npossible, the vcpkg package manager is used. The package manager should \nhandle all build dependencies PyMOL needs.\n\n### Edited \u0026 alternative design\nTo honor Warren L. DeLano the original creator of PyMOL an alternative \nlogo can be used as well as an alternate splash screen. The logo is only altered\nin its color and the splash screen is inspired by early PyMOL versions of \nWarren himself.\n\n## Build\n### Wheel file\n#### Pre-built _cmd module\nTo build the wheel file (based on the provided pre-built `_cmd` module), follow these steps (the working directory is the repository root directory):\n\n1. Set up a Python virtual environment under the project root directory.\n\n2. Install all requirements using the requirements.txt:\n    ```shell\n    pip install -r requirements.txt\n    ```\n\n3. Set up the build environment by running:\n   ```shell\n   ./run_automation.sh setup-dev-env\n   ```\n\n4. Build the wheel file using the pre-built `_cmd` module\n    ```shell\n    ./run_automation.sh build-wheel\n    ```\n    After a successful build the wheel file can be found under the `dist/` folder.\n\n\n#### Self built _cmd module\nAfter you have built the `_cmd` module yourself you can run the following command \nto build the wheel file:\n```shell\n./run_automation.sh build-wheel\n```\nAfter a successful build the wheel file can be found under the `dist/` folder.\n\nFeel free to contribute or test the files as needed.\n\n### From source\n#### Prerequisites:\n- CMake\n    - **Be aware**: Add the cmake to your PATH variable. Check by running `cmake --version`\n- Ubuntu:\n    ```shell\n    sudo apt update -y \u0026\u0026 sudo apt-get install git build-essential python3.11-dev libglew-dev libpng-dev libfreetype6-dev libxml2-dev libmsgpack-dev python3-pyqt5.qtopengl libglm-dev libnetcdf-dev autoconf\n    ```\n\n#### Step-by-step guide\n1. Load the CMake project (e.g. in PyCharm right-click on the CMakeLists.txt file \nand select `Load CMake Project`)\n2. Create a `Release` CMake build profile (e.g. in PyCharm click on the CMake \nicon in the bottom left panel and click on the `Gear icon \u003e CMake Settings`)\n3. Add the following line to your CMake build profile:\n    ```shell\n    -DCMAKE_TOOLCHAIN_FILE=$CMakeProjectDir$/vendor/vcpkg/scripts/buildsystems/vcpkg.cmake\n    ```\n4. Build the project.\n5. **Optional**: If you now run `./run_automation.sh build-wheel` the new \nwheel file will automatically use your self built `_cmd` module.\n\n## Roadmap\nUntil now the build wheel file can only be used with Python 3.11.\nThe plan for the future is to support multiple different Python versions.\n\n## Acknowledgements\n**Schrödinger** for being the driving force behind the continued development of PyMOL after Warren's passing, ensuring that the open-source version remained alive and well. \n\n**NOTE**: the following list has not been updated since Fall 2003.  \nSince then, the PyMOL effort has grown to such an extent that it is no longer\npractical to recognize everyone individually.  Fortunately, a public\nrecord of participation exists and can be appreciated on the internet,\nand especially via the PyMOL mailing list archives.  Suffice it to say\nthat the PyMOL user community now numbers well into the thousands and\nincludes scientists, students, and educators worldwide, spread\nthroughout academia and the biotechnology and pharmaceutical\nindustries.  Though DeLano Scientific LLC specifically supports and\nmaintains the PyMOL code base, the project can only continue to\nsucceed through the sponsorship and participation of the broader\ncommunity.\n\n**Founder and Principal Author**:\n\n      Warren L. DeLano \n\nMajor Authors (5000+ lines of code):\n\n      Ralf W. Grosse-Kunstleve (SGLite Module)\n\nMinor Authors (500+ lines of code):\n\n      Scott Dixon (Metaphorics CEX support)\n      Filipe Maia (Slice Objects)\n\nOther Contributors: These are the people who have gone out of\ntheir way to help the project with their ideas, actions,\nadvice, hardware donations, testing, information, sponsorship,\npeer support, or code snippets.\n\n      Daan van Aalten\n      Paul Adams \n      Stephen Adler\n      Jun Aishima \n      Dennis Allison\n      Ricardo Aparicio\n      Daniel Appelman   \n      Diosdado \"Rey\" Banatao\n      Michael Banck\n      Ulrich Baumann\n      Joseph Becker\n      Balaji Bhyravbhatla\n      Jeff Bizzaro\n      Jeff Blaney \n      Juergen Bosch \n      Michael Bower\n      Sarina Bromberg\n      Axel Brunger\n      Robert Campbell\n      Bronwyn Carlisle \n      Duilio Cascio\n      Julien Chiron \n      Shawn Christensen\n      Scott Classen\n      David Cooper\n      Larry Coopet\n      Jacob Corn\n      Ben Cornett\n      Andrew Dalke \n      Koen van der Drift \n      Harry Dailey\n      Byron DeLaBarre\n      Bill DeGrado\n      Thomas Earnest\n      Nathaniel Echols\n      John Eksterowicz\n      Erik Evensen\n      David Fahrney\n      Tim Fenn\n      Thierry Fischmann\n      Michael Ford\n      Esben Peter Friis\n      Kevin Gardner\n      R. Michael Garavito\n      John Gerig\n      Jonathan Greene\n      Michael Goodman  \n      Joel Harp\n      Reece Hart\n      Richard Hart\n      Peter Haebel\n      Matt Henderson\n      Douglas Henry \n      Possu Huang \n      Uwe Hoffmann\n      Jenny Hinshaw\n      Carly Huitema\n      Bjorn Kauppi\n      Greg Landrum\n      Robert Lawrence Kehrer \n      Tom Lee\n      Eugen Leitl\n      Ken Lind\n      Jules Jacobsen\n      Luca Jovine\n      Andrey Khavryuchenko\n      David Konerding\n      Greg Landrum\n      Michael Love \n      Tadashi Matsushita\n      Genevieve Matthews \n      Gerry McDermott \n      Robert McDowell\n      Gustavo Mercier      \n      Naveen Michaud-Agrawal\n      Aaron Miller\n      Holly Miller\n      Tim Moore\n      Kelley Moremen\n      Hideaki Moriyama\n      Nigel Moriarty \n      Geoffrey Mueller\n      Cameron Mura\n      Florian Nachon \n      Hanspeter Niederstrasser \n      Michael Nilges\n      Hoa Nguyen\n      Shoichiro Ono\n      Chris Oubridge\n      Andre Padilla\n      Jay Pandit\n      Ezequiel \"Zac\" Panepucci\n      Robert Phillips\n      Hans Purkey\n      Rama Ranganathan\n      Michael Randal\n      Daniel Ricklin \n      Ian Robinson\n      Eric Ross\n      Kristian Rother\n      Marc Saric\n      Bill Scott\n      Keana Scott\n      Denis Shcherbakov\n      Goede Schueler\n      Paul Sherwood\n      Ward Smith\n      John Somoza\n      David van der Spoel\n      Paul Sprengeler\n      Matt Stephenson \n      Peter Stogios\n      John Stone\n      Charlie Strauss\n      Michael Summers\n      Brian Sutton\n      Hanna and Abraham Szoke\n      Rod Tweten\n      Andras Varadi\n      Scott Walsh\n      Pat Walters\n      Mark White\n      Michael Wilson\n      Dave Weininger\n      Chris Wiesmann\n      Charles Wolfus\n      Richard Xie\n\nMiscellaneous Code Snippets Lifted From:\n\n      Thomas Malik (fast matrix-multiply code)\n      John E. Grayson (Author of \"Python and Tkinter\")\n      Doug Hellmann (Wrote code that JEG later modified.)\n\nOpen-Source \"Enablers\" (essential, but not directly involved):\n\n      Brian Paul (Mesa)\n      Mark Kilgard (GLUT)\n      Guido van Rossum (Python)\n      Linus Torvalds (Linux Kernel)\n\n      Precision Insight (DRI)\n      The XFree86 Project (Free Windowing System)\n      VA Linux (CVS Hosting)\n      Richard Stallman/Free Software Foundation (GNU Suite)\n      The unknown authors of EISPACK (Linear Algebra)\n\nGraphics Technology \"Enablers\" (essential!)\n\n      3dfx (RIP)\n      nVidia \n      ATI\n\n### Specific Acknowledgments:\n\n* Thanks to Joni W. Lam for making the business work.\n\n* Thanks to John Stone and John Furr for being such excellent\n  colleagues.\n\n* Thanks to Ragu Bharadwaj and Marcin Joachimiak for Java expertise\n  and encouragement.\n\n* Thanks to Apple Computer for continued encouragement, assistance,\n  and HLAs in support of Mac development.  Thanks especially to\n  Robert Kehrer for creating so many fun opportunities over the years.\n\n* Thanks to Aaron Miller (GlaxoSmithKline) for a continuous stream of\n  thoughtful opinions and suggestions.\n\n* Thanks to Dave Weininger for suggesting the \"roving\" feature and for\n  being such an inspirational friend and mentor.\n\n* Thanks to Matt Hahn and Dave Rogers for proving that it can also be\n  done, again.\n\n* Thanks to Mick Savage for providing experienced practical advice on\n  the marketing of scientific software.\n\n* Thanks to Ian Matthew for 3D experience and perspective.\n\n* Thanks for Jeff Blaney for numerous insightful discussions.\n\n* Thanks to Elizabeth Pehrson for making this a team effort.\n\n* Thanks to Erin Bradley for schooling in focus and vision.\n\n* Thanks to Vera Povolona for catalytic clarity and introspection.\n\n* Thanks to Anthony Nichols for proving that it can be done, yet again.\n\n* Thanks to Thompson Doman for timely Open-Source validation.\n\n* Thanks to Manfred Sippl for making it all seem so simple.\n\n* Thanks to Kristian Rother for all his excellent work building on the\n  PyMOL foundation, and in helping others learn to use the software.\n\n* Thanks to Dave Weininger, Scott Dixon, Roger Sayle, Andrew Dalke,\n  Anthony Nichols, Dick Cramer, and David Miller, as well as rest of\n  the Daylight and OpenEye teams for thoughtful discussions on PyMOL\n  and open-source software during my 2002 pilgrimage to Sante Fe, NM.\n\n* Thanks to Ralf Grosse-Kunstleve for his contribution of the \"sglite\"\n  space group and symmetry handling module.\n\n* Thanks to the scientists and management of Sunesis Pharmaceuticals\n  for supporting PyMOL development since program inception.\n\n* Thanks to the Computational Crystallography Initiative (LBNL)\n  developers for their encouragement, ideas, and support.\n\n* Thanks to Scott Walsh for being the first individual to provide\n  financial support for PyMOL.\n\n* Thanks to the hundreds of individuals, companies, and institutions\n  that have provided financial support for the project.\n\n* Thanks to Brian Paul and the Precision Insight team for development\n  of Mesa/DRI which greatly assisted in the early development of PyMOL.\n\n* Thanks to Michael Love for the first major outside port of PyMOL\n  (to GNU-Darwin/OSX) and for believing in the cause.\n\n* Thanks for Paul Sherwood for making a concerted effort to develop\n  using PyMOL long before the software and vision had matured.\n\n* Thanks to Jay Ponder for thoughtful email discussions on Tinker and\n  the role of open-source scientific software.\n\n* Thanks to hundreds of PyMOL users for the many forms of feedback,\n  bug sightings, and encouragement they've provided.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Furban233%2Fpymol-open-source-linux-build","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Furban233%2Fpymol-open-source-linux-build","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Furban233%2Fpymol-open-source-linux-build/lists"}