Windows Install

From PyMOLWiki
Jump to: navigation, search



Pre-compiled PyMOL

Pre-compiled PyMOL is available free from Christoph Gohlke of the Laboratory for Fluorescence Dynamics, University of California, Irvine here.

  1. Install python, 2.7 for windows. Use the standard options.
  2. Download appropriate installer and select according to your python version 2.7 and 32/64 bit system.
  3. Run the downloaded installer
  4. PyMOL is now installed in: C:\Python27\PyMOL
  5. Run PyMOL by executing: C:\Python27\PyMOL\PyMOL.cmd

You should make a shortcut to the PyMOL.cmd tile and place in your Start menu.
If you right-click a .pdb file, and "Open with", and then point to C:\Python27\PyMOL\PyMOL.cmd, you can double click .pdb files.

Extend PyMOL with additional scripts

If you now want to extend the capabilities of PyMOL, and take advantage of all the available plugins+scripts "out there", then do the following.

  1. First install "numpy" as an available module to Python. Select appropriate installer from here
  2. Download the script/plugin collection Pymol-script-repo from a .zip file from here
git clone
  1. Unpack it to here: C:\Python27\Lib\site-packages\pymol\pymol_path\Pymol-script-repo Double check that the folder name is correct and the same.

Open "Notepad" and write.

# Add paths to sys.path so PyMOL can find modules and scripts
import sys, os
pymol_git = os.path.abspath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))
os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
# Make setting changes to Plugin Manager
import pymol.plugins
pymol.plugins.preferences = {'instantsave': False, 'verbose': False}
pymol.plugins.autoload = {'apbs_tools': False}
pymol.plugins.set_startup_path([os.path.join(pymol_git, 'plugins'), os.path.join(sys.prefix, 'Lib', 'site-packages', 'pmg_tk', 'startup')])
pymol.plugins.preferences = {'instantsave': True, 'verbose': False}

Then "File->Save as->All files-> C:\Python27\Lib\site-packages\pymol\pymol_path\

Now start pymol, and enjoy all the plugins available from the menu.

PyMoL shortcut
Make a pymol directory in your homepath. mkdir %HOMEPATH%\pymol Then make sure, PyMOL starts here, when you open the shortcut.
Make a shotcut to the .cmd file, and modify it.
Target: C:\python27\PyMOL\pymol.cmd
Start in: %HOMEPATH%\pymol

Personal changes to opening of PyMOL

You can make a "pymolrc.pym" file, and put it under "C:\Users\YOU".
In the file you can write things that PyMOL should change from standard values, when it opens.
See more here.


To install PyMOL from the binaries, just run the executable you've downloaded.


To get the latest features, you should download the PyMOL source from the project page.

Directions using CygWin

You should have similar packages installed as described here. Note, that you might need gcc-4.4 instead of gcc-4.5.

Personal tools