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This repository offers **unofficial** setups/packages for the open-source version of PyMOL(TM)

for **all major** operating systems.

* [About PyMOL](#About-PyMOL)

* [Contents of this repository](#Contents-of-this-repository)

* [Scripts](#Scripts)

* [From source](#From-source)

* [Prerequisites](#Prerequisites)

* [Step-by-step guide](#Step-by-step-guide)

* [License](#License)

* [Acknowledgements](#Acknowledgements)

[PyMOL™](https://pymol.org/) is a powerful visualization software for rendering and animating 3D molecular structures. PyMOL is a trademark of Schrödinger, LLC.

Please 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."

"Insert some more information here"

The following information is about building a platform dependent package/setup from source.

- Inno Setup compiler 6

- Install location must be: `C:\Program Files (x86)\Inno Setup 6\ISCC.exe`

- Ruby (**only** if fpm is used for packaging)

- apt (Debian or Ubuntu): `sudo apt-get install ruby-full`

- yum (CentOS, Fedora, or RHEL): `sudo yum install ruby`

1. Create a new Python virtual environment

2. Install build dependencies using the requirements.txt of your platform

3. Build the app package:

If you are on Windows run:

.\win_automator.bat build app

.\win_automator.bat build inno_setup

If you are on macOS:

chmod +x ./automator.sh && ./automator.sh build app

To build the DMG use a tool like [create-dmg](https://github.com/create-dmg/create-dmg) or fork the repository

and run the GitHub action build_app.yaml.

If you are on Linux:

chmod +x ./automator.sh && ./automator.sh build app

To build the tar.gz run:

mkdir -p packaged/build/Open-Source-PyMOL-<version-number>

cp -r ./dist/exe.linux*/* packaged/build/Open-Source-PyMOL-<version-number>/

mkdir -p packaged/bin

tar czvf packaged/bin/Open-Source-PyMOL-<version-number>.tar.gz packaged/build/Open-Source-PyMOL-<version-number>

If you want to build a .deb or .rpm package, you could use the Ruby gem called fpm:

sudo gem install fpm

mkdir -p package-root/opt/Open-Source-PyMOL-<version-number>

cp -r ./dist/exe.linux*/* package-root/opt/Open-Source-PyMOL-<version-number>/

mkdir -p package-root/usr/bin

ln -s /opt/Open-Source-PyMOL-<version-number>/Open-Source-PyMOL package-root/usr/bin/Open-Source-PyMOL

mkdir -p package-root/usr/share/applications

cp os_specific/linux/open-source-pymol.desktop package-root/usr/share/applications

fpm -s dir -t deb \

-n open-source-pymol \

-v <version-number> \

-a amd64 \

-C package-root \

--description "PyMOL installation for debian-based distros" \

--license "BSD-3-Clause" \

Copyright (c) [Schrodinger, LLC](https://www.schrodinger.com/)

Published under a BSD-like license, see [LICENSE](LICENSE).

**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.

**NOTE**: the following list has not been updated since Fall 2003 and was originally created by Warren himself.

Since then, the PyMOL effort has grown to such an extent that it is no longer

practical to recognize everyone individually. Fortunately, a public

record of participation exists and can be appreciated on the internet,

and especially via the PyMOL mailing list archives. Suffice it to say

that the PyMOL user community now numbers well into the thousands and

includes scientists, students, and educators worldwide, spread

throughout academia and the biotechnology and pharmaceutical

industries. Though DeLano Scientific LLC specifically supports and

maintains the PyMOL code base, the project can only continue to

succeed through the sponsorship and participation of the broader

community.

**Founder and Principal Author**:

Warren L. DeLano

Major Authors (5000+ lines of code):

Ralf W. Grosse-Kunstleve (SGLite Module)

Minor Authors (500+ lines of code):

Scott Dixon (Metaphorics CEX support)

Filipe Maia (Slice Objects)

Other Contributors: These are the people who have gone out of

their way to help the project with their ideas, actions,

advice, hardware donations, testing, information, sponsorship,

peer support, or code snippets.

Daan van Aalten

Paul Adams

Stephen Adler

Jun Aishima

Dennis Allison

Ricardo Aparicio

Daniel Appelman

Diosdado "Rey" Banatao

Michael Banck

Ulrich Baumann

Joseph Becker

Balaji Bhyravbhatla

Jeff Bizzaro

Jeff Blaney

Juergen Bosch

Michael Bower

Sarina Bromberg

Axel Brunger

Robert Campbell

Bronwyn Carlisle

Duilio Cascio

Julien Chiron

Shawn Christensen

Scott Classen

David Cooper

Larry Coopet

Jacob Corn

Ben Cornett

Andrew Dalke

Koen van der Drift

Harry Dailey

Byron DeLaBarre

Bill DeGrado

Thomas Earnest

Nathaniel Echols

John Eksterowicz

Erik Evensen

David Fahrney

Tim Fenn

Thierry Fischmann

Michael Ford

Esben Peter Friis

Kevin Gardner

R. Michael Garavito

John Gerig

Jonathan Greene

Michael Goodman

Joel Harp

Reece Hart

Richard Hart

Peter Haebel

Matt Henderson

Douglas Henry

Possu Huang

Uwe Hoffmann

Jenny Hinshaw

Carly Huitema

Bjorn Kauppi

Greg Landrum

Robert Lawrence Kehrer

Tom Lee

Eugen Leitl

Ken Lind

Jules Jacobsen

Luca Jovine

Andrey Khavryuchenko

David Konerding

Greg Landrum

Michael Love

Tadashi Matsushita

Genevieve Matthews

Gerry McDermott

Robert McDowell

Gustavo Mercier

Naveen Michaud-Agrawal

Aaron Miller

Holly Miller

Tim Moore

Kelley Moremen

Hideaki Moriyama

Nigel Moriarty

Geoffrey Mueller

Cameron Mura

Florian Nachon

Hanspeter Niederstrasser

Michael Nilges

Hoa Nguyen

Shoichiro Ono

Chris Oubridge

Andre Padilla

Jay Pandit

Ezequiel "Zac" Panepucci

Robert Phillips

Hans Purkey

Rama Ranganathan

Michael Randal

Daniel Ricklin

Ian Robinson

Eric Ross

Kristian Rother

Marc Saric

Bill Scott

Keana Scott

Denis Shcherbakov

Goede Schueler

Paul Sherwood

Ward Smith

John Somoza

David van der Spoel

Paul Sprengeler

Matt Stephenson

Peter Stogios

John Stone

Charlie Strauss

Michael Summers

Brian Sutton

Hanna and Abraham Szoke

Rod Tweten

Andras Varadi

Scott Walsh

Pat Walters

Mark White

Michael Wilson

Dave Weininger

Chris Wiesmann

Charles Wolfus

Richard Xie

Miscellaneous Code Snippets Lifted From:

Thomas Malik (fast matrix-multiply code)

John E. Grayson (Author of "Python and Tkinter")

Doug Hellmann (Wrote code that JEG later modified.)

Open-Source "Enablers" (essential, but not directly involved):

Brian Paul (Mesa)

Mark Kilgard (GLUT)

Guido van Rossum (Python)

Linus Torvalds (Linux Kernel)

Precision Insight (DRI)

The XFree86 Project (Free Windowing System)

VA Linux (CVS Hosting)

Richard Stallman/Free Software Foundation (GNU Suite)

The unknown authors of EISPACK (Linear Algebra)

Graphics Technology "Enablers" (essential!)

3dfx (RIP)

nVidia

ATI

* Thanks to Joni W. Lam for making the business work.

* Thanks to John Stone and John Furr for being such excellent

colleagues.

* Thanks to Ragu Bharadwaj and Marcin Joachimiak for Java expertise

and encouragement.

* Thanks to Apple Computer for continued encouragement, assistance,

and HLAs in support of Mac development. Thanks especially to

Robert Kehrer for creating so many fun opportunities over the years.

* Thanks to Aaron Miller (GlaxoSmithKline) for a continuous stream of

thoughtful opinions and suggestions.

* Thanks to Dave Weininger for suggesting the "roving" feature and for

being such an inspirational friend and mentor.

* Thanks to Matt Hahn and Dave Rogers for proving that it can also be

done, again.

* Thanks to Mick Savage for providing experienced practical advice on

the marketing of scientific software.

* Thanks to Ian Matthew for 3D experience and perspective.

* Thanks for Jeff Blaney for numerous insightful discussions.

* Thanks to Elizabeth Pehrson for making this a team effort.

* Thanks to Erin Bradley for schooling in focus and vision.

* Thanks to Vera Povolona for catalytic clarity and introspection.

* Thanks to Anthony Nichols for proving that it can be done, yet again.

* Thanks to Thompson Doman for timely Open-Source validation.

* Thanks to Manfred Sippl for making it all seem so simple.

* Thanks to Kristian Rother for all his excellent work building on the

PyMOL foundation, and in helping others learn to use the software.

* Thanks to Dave Weininger, Scott Dixon, Roger Sayle, Andrew Dalke,

Anthony Nichols, Dick Cramer, and David Miller, as well as rest of

the Daylight and OpenEye teams for thoughtful discussions on PyMOL

and open-source software during my 2002 pilgrimage to Sante Fe, NM.

* Thanks to Ralf Grosse-Kunstleve for his contribution of the "sglite"

space group and symmetry handling module.

* Thanks to the scientists and management of Sunesis Pharmaceuticals

for supporting PyMOL development since program inception.

* Thanks to the Computational Crystallography Initiative (LBNL)

developers for their encouragement, ideas, and support.

* Thanks to Scott Walsh for being the first individual to provide

financial support for PyMOL.

* Thanks to the hundreds of individuals, companies, and institutions

that have provided financial support for the project.

* Thanks to Brian Paul and the Precision Insight team for development

of Mesa/DRI which greatly assisted in the early development of PyMOL.

* Thanks to Michael Love for the first major outside port of PyMOL

(to GNU-Darwin/OSX) and for believing in the cause.

* Thanks for Paul Sherwood for making a concerted effort to develop

using PyMOL long before the software and vision had matured.

* Thanks to Jay Ponder for thoughtful email discussions on Tinker and

the role of open-source scientific software.

* Thanks to hundreds of PyMOL users for the many forms of feedback,

bug sightings, and encouragement they've provided.

Install location: `/opt/open-source-pymol`