----------------------------------------------------------------------
This is a patched branch of the PyMOL open source tree and is
considered experimental code. If you are looking for the upstream
project, please visit:

    https://sourceforge.net/projects/pymol

This branch has:
  * Several patches applied from the bug tracker at sourceforge.net
  * A setup.py which makes setup2.py obsolete
  * VMD plugins enabled by default
----------------------------------------------------------------------

INSTALL

    prefix=/opt/pymol-git
    python setup.py build install \
        --home=$prefix \
        --install-lib=$prefix/modules \
        --install-scripts=$prefix

CHECKOUT WITH UPSTREAM BRANCH

    git svn clone -r 4001 https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol.git
    cd pymol.git
    git branch upstream
    git remote add origin git@github.com:speleo3/pymol.git
    git pull origin master

UPDATE FROM SVN

    git checkout upstream && git svn rebase && git checkout master
    git merge -m 'Merge upstream svn' upstream

DIFF TO SVN

    git diff git-svn

----------------------------------------------------------------------
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
      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
      
----------------------------------------------------------------------
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.