is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.
| README (pymol-v2.1.0.tar.bz2) | : | README (pymol-open-source-2.2.0) |
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| PyMOL is Copyright (c) Schrodinger, LLC | | |
| http://www.pymol.org | | |
| PyMOL is an OPEN SOURCE program distributed under the "Python" license. | | |
| Please see the LICENSE file for additional information. | | |
| See INSTALL for installation instructions | | |
| PyMOL has the following external dependencies: | | |
| 1. OpenGL | | |
| 2. GLUT library for OpenGL (or freeglut) | | |
| 3. Python (v 2.1 or better) compiled with threads support | | |
| 4. libpng (can compiled without it, but image saves won't work) | | |
| 5. Tcl/Tk (for the external GUI) | | |
| 6. Numerical Python (technically optional - now using numpy instead) | | |
| 7. Python megawidgets (Pmw -- only required for the "external" GUI) | | |
| 8. FreeType2 (if you want nice fonts) | | |
| The PyMOL Team: | | |
| | |
| NOTE: this list has not been updated since Fall 2003. 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 Schrodinger, 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 -- inactivated as of 2008) | | |
| | |
| 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 | | Contrib Directory Disclaimer Notice |
| 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 | | |
| | |
|
| | All software in the PyMOL "contrib" directory is either under a |
| | PyMOL-compatible BSD-like unrestricted open-source license or has been |
| | released under terms which specifically permit inclusion with PyMOL. |
| | Schrodinger, LLC believes that you have permission to use the |
| | code contained herein with PyMOL without incurring any additional |
| | costs or obligations, but we do not warrant or guarantee this |
| | assertion. |
| | |
| | ---------------------------------------------------------------------- |
| | USE OF PYMOL CONTRIB SOFTWARE IS ENTIRELY AT YOUR OWN RISK. |
| | |
| | SCHRODINGER, LLC DISCLAIM ALL WARRANTIES |
| | WITH REGARD TO PYMOL CONTRIB SOFTWARE, INCLUDING ALL IMPLIED |
| | WARRANTIES OF MERCHANTABILITY, FITNESS, OWNERSHIP, AND NONINFRINGEMENT |
| | OF THIRD PARTY RIGHTS. IN NO EVENT SHALL |
| | SCHRODINGER, LLC BE LIABLE FOR ANY SPECIAL, INDIRECT OR |
| | CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF |
| | USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR |
| | OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR |
| | PERFORMANCE OF PYMOL CONTRIB SOFTWARE. |
| | |
| | Individual contrib packages are protected under the copyrights of |
| | their respective authors. Please see the source code and any LICENSE |
| | or COPYING files for specific information regarding each contrib |
| | package. |
| ---------------------------------------------------------------------- | | ---------------------------------------------------------------------- |
|
| Specific Acknowledgments (last updated around 2005): | | |
| | |
| * 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. | | |
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"Fossies" - the Fresh Open Source Software Archive 