Jan Gebauer.de

Another version of PyMol (1.3r1) has been released.

Unfortunately, with every new version the trouble of compiling it for windows is getting bigger and bigger… I do have teh feeling that this is -at least- knowingly accepted by the releasers.

However, after a couple of hours fiddling around with the installation routine, I was able to update my guide to the new version. Have fun and let me know, if it works for you!

Jan

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

1. There is an old but executable version of PyMol freely available here.
2. 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

1. 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)]:
   1. G++ (gcc-g++)
   2. Python (python, phyton-tkinter)
   3. openGL (openGL)
   4. PNG (libPNG12, libPNG12-devel)
   5. TCL/Tk libaries (tcltk)
2. Download source codes for PyMol  http://pymol.svn.sourceforge.net/viewvc/pymol/trunk.tar.gz?view=tar and extract it to c:\pymol
3. Replace the setup.py in c:\pymol\ with the file in this archive.
4. Start the “Cygwin bash shell” form the Windows start menu and change to the pymol directory by typing

cd c:/pymol

5. Compile PyMol using following commands in the cygwin command line:

python setup.py build install
python setup2.py install

6. Copy “pymol” to usr/bin or similar

cp pymol /usr/bin

7. Download PMW (http://pmw.sourceforge.net/)
8. Copy files to temporary directory (e.g. C:\temp\)
9. Install PMW using

 cd C:\temp\mw1.3.2\src\
 pyhton setup.py install
 

10. 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:

1. The PyMol Wiki
2. The “How to use PyMOL” presentation of Stephen Curry’s homepage
3. 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:

1. 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.