Windows Install

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This page describes how to install PyMOL on Microsoft Windows.

Incentive PyMOL

Schrödinger provides an installer to paying sponsors (EXE for PyMOL 2.0, MSI for previous version). The bundle also includes ready-to-use APBS, RigiMOL, an MPEG encoder for movie export, and a small molecule energy minimization engine.

Download: https://pymol.org/#download

Open-Source PyMOL

Open-Source PyMOL is available free of charge. It also allows sponsors to create highly customized PyMOL installations which might not be possible with the MSI installer.

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

  1. Install the latest version of Python 3 for Windows (e.g., by going to http://www.python.org/downloads/ and choosing the x64 EXE installer). Use the standard options, which should mean that the installation directory is most likely C:\Users\<Your Username>\AppData\Local\Programs\Python\Python38). Make sure the option to add environment variables is selected.
  2. Download the appropriate wheel files, along with all requirement wheel files (including pip, Numpy and PMW) into a single file directory, e.g., C:\Users\<Your Username>\Downloads\PyMOL_installation

Navigate to the installation directory in a CMD window

cd C:\Users\<Your Username>\Downloads\PyMOL_installation

(or where ever you put the files) and begin the installation using the command:

python.exe pip-20.x.x-py2.py3-none-any.whl/pip install --no-index --find-links="%CD%" pymol_launcher

If your python install is part of your PATH variable, then running (where x refers to the version number of pip):

python pip-20.x.x-py2.py3-none-any.whl/pip install --no-index --find-links="%CD%" pymol_launcher

should suffice.

To update PyMOL update the files in the PyMOL install directory and run:

pip install --upgrade --no-deps pymol.whl

where pymol.whl is replaced by the PyMOL wheel file name (not the launcher, the launcher should not require updating). To use the newer single-window Qt interface, also install the optional PyQt5 dependency for your Python installation:

 pip install pyqt5

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 https://github.com/Pymol-Scripts/Pymol-script-repo
  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')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])

# 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\run_on_startup.py

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 shortcut to the .cmd file, and modify it.
Target: C:\python27\PyMOL\pymol.cmd
Start in: %HOMEPATH%\pymol

See Also