Editing Windows Install (section)

=== 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. <br>
# First install "numpy" as an available module to Python. [https://github.com/cgohlke/numpy-mkl-wheels/ Select appropriate installer from here]
# Download the script/plugin collection [[Git | Pymol-script-repo]] from [https://github.com/Pymol-Scripts/Pymol-script-repo/zipball/master a .zip file from here]
 git clone https://github.com/Pymol-Scripts/Pymol-script-repo
# 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.
<syntaxhighlight lang="python">
# 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}
</syntaxhighlight>
'''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<br>
Make a '''pymol''' directory in your homepath. '''mkdir %HOMEPATH%\pymol'''  Then make sure, PyMOL starts here, when you open the shortcut.<br>
Make a shortcut to the .cmd file, and modify it. <br>
Target: C:\python27\PyMOL\pymol.cmd <br>
Start in: %HOMEPATH%\pymol