Editing Windows Install (section)

== Open-Source PyMOL ==

Open-Source PyMOL is available [https://github.com/schrodinger/pymol-open-source/blob/master/LICENSE free of charge]. It also allows sponsors to create highly customized PyMOL installations which might not be possible with the MSI installer.

=== One-click Installer ===
A convenient and easy-to-use one-click installer is available that runs out-of-the-box without the need for an existing Python installation. You can download it [https://github.com/kullik01/pymol-open-source-setup/releases/download/v3.1.0.4%2B1/PyMOL_Open_source_v3.1.0.4+1_WINx64_setup.exe here] or go to the [https://github.com/kullik01/pymol-open-source-setup GitHub repository] and then to [https://github.com/kullik01/pymol-open-source-setup/releases/tag/v3.1.0.4%2B1 Releases]. It features an alternate splash screen and a slightly updated menu stylesheet.

=== Pre-compiled Open-Source PyMOL ===

Pre-compiled Open-Source PyMOL is available free from [https://www.cgohlke.com/ Christoph Gohlke of the Laboratory for Fluorescence Dynamics, University of California, Irvine].

# 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 or add the folder of python.exe to system PATH.
# Install [https://support.microsoft.com/en-us/help/2977003/the-latest-supported-visual-c-downloads the current Microsoft Visual C++ Redistributable for Visual Studio 2015, 2017 and 2019]. Otherwise the installed PyMOL binary may fail to run (without any error message!).
## Have a look in "Add/Remove" programs if it's installed already
# Download the [https://github.com/cgohlke/pymol-open-source-wheels/ appropriate wheel files], along with all requirement wheel files ([https://github.com/cgohlke/numpy-mkl-wheels/ Numpy+MKL]) into a single file directory, e.g., <code>C:\Users\<Your Username>\Downloads</code>
# Example of filenames 2023-01-12
## pymol_launcher-2.5-cp311-cp311-win_amd64.whl
## pymol-2.6.0a0-cp311-cp311-win_amd64.whl
## numpy-1.22.4+mkl-cp311-cp311-win_amd64.whl

Navigate to the installation directory in a CMD window (Not PowerShell!) <source lang = python>cd C:\Users\<Your Username>\Downloads</source> (or where ever you put the files) and begin the installation using the command: ("%CD%" only works in CMD) 
<source lang = python>
python -m pip pmw
python -m pip install --no-index --find-links="%CD%" pymol_launcher-2.5-cp311-cp311-win_amd64.whl
where.exe pymol
pymol
</source>

PyMOL.exe should now be in C:\Users\<Your Username>\AppData\Local\Programs\Python

To use the newer single-window Qt interface, also install the optional PyQt5 dependency for your Python installation: 
<source lang=python>
python -m pip install pyqt5
</source>

To update PyMOL update the files in the PyMOL install directory and run: 
<source lang = python>
pip install --upgrade --no-deps pymol.whl
</source> 
where <code>pymol.whl</code> is replaced by the PyMOL wheel file name (not the launcher, the launcher should not require updating). 

=== Building from source ===
This [https://github.com/urban233/pymol-open-source-windows-build GitHub repository] provides the tools to build PyMOL for Windows from source. It automatically downloads all necessary dependencies via the vcpkg package manager. You can either build the complete wheel file or just the _cmd C/C++ extension module using the provided automation script. A pre-built wheel file is available for download directly from the [https://github.com/urban233/pymol-open-source-windows-build/releases/tag/v3.1.0a0 Releases] tab.

=== 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