2nd Update:
A(nother) new version of PyMol needed a couple of updates to the method outlined below. The following method works as of 02.09.2010 with PyMol 1.3r1 (Revision 3911) and cygwin (1.7.7-1) . Please let me know if you have any trouble.
There are many program out on the market for visualising three dimensional structure: SwissPDB-Viewer, Rasmol and Jmol, just to name a few. They all have their advantages; however, in recent years PyMol seems to have established itself as the leading standard for the generation of high quality figures for publications.
PyMol is a user-sponsored open-source project originally created by Warren Lyford DeLano and continued after his early death by Schrödinger. Open-source means everyone can get the source code of the program to make his own version, user-sponsored means you have to pay if you want an executable (meaning: a running version). For Linux users it’s normally no a big problem to generate a running program from the sources, but on Windows systems this is mostly a hassle. The following guide will take you through every step needed to generate an up-to-date version of PyMol running on Windows.
Preliminary remark
- There is an old but executable version of PyMol freely available here.
- There are different ways to build PyMol on Windows. The way I describe it here is “quick-and-dirty”. You probably can do it with little knowledge about your PC; however, you don’t get a “real” Windows program and you can’t easily give the program to others. If you want to do it the “hard” way have a look here, but I wouldn’t recommend it if you are not an PC expert.
Compiling / Building PyMol
- Download and install Cygwin (http://www.cygwin.com/). In additional to the standard packages select the following packages during the installation routine [program (package titles)]:
- G++ (gcc-g++)
- Python (python, phyton-tkinter)
- openGL (openGL)
- PNG (libPNG12, libPNG12-devel)
- TCL/Tk libaries (tcltk)
- Download source codes for PyMol http://pymol.svn.sourceforge.net/viewvc/pymol/trunk.tar.gz?view=tar and extract it to c:\pymol
- Replace the setup.py in c:\pymol\ with the file in this archive.
- Start the “Cygwin bash shell” form the Windows start menu and change to the pymol directory by typing
cd c:/pymol
- Compile PyMol using following commands in the cygwin command line:
python setup.py build install
python setup2.py install
- Copy “pymol” to usr/bin or similar
cp pymol /usr/bin
- Download PMW (http://pmw.sourceforge.net/)
- Copy files to temporary directory (e.g. C:\temp\)
- Install PMW using
cd C:\temp\mw1.3.2\src\
pyhton setup.py install
- finished
You should now be able to start the program by typing .\pymol in the “Cygwin bash screen”.
Tip: To get a Windows shortcut to PyMol, generate a shortcut on your desktop (via right-click->New->Shortcut) and enter the following as target:
C:\cygwin\bin\run.exe "bash" "/usr/bin/pymol"
There are plenty of resources available for how to use PyMol. Here a few nice sites:
- The PyMol Wiki
- The “How to use PyMOL” presentation of Stephen Curry’s homepage
- The PyMol Tutorial of KB Wong
I’m looking forward to comments, suggestions and possible problems you have with this guide.
Known problems with this guide:
- Clipping with the mouse wheel does not work. SHIFT-Left-Click and moving the mouse does the clipping fine, however. Look here for a quick tutorial.
