JP's Notes

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====== Install PyMOL on Windows ======

If you are on Ubuntu, installing PyMOL is as easy as ''sudo apt-get install pymol''.  Unfortunately, almost all students in my medicinal biochemistry course use Windows as their OS (why?!).  This page contains a "followable" set of instructions to install PyMOL on Windows.  Note that you could use the [[https://pymol.org/2/|PyMOL installation]] from Schrodinger, but you need a paid licence for that (yuck!).


===== Installing the Python Interpreter =====

So, first we a Python interpreter.  PyMOL is written in the Python programming language, hence you need this to run PyMOL.

  - Download Python 3.9.2 (the minor version - the last number - may change) from the [[https://www.python.org/downloads/windows/|Python website]] (the file you want is under in link ''Windows installer (64-bit)'').
  - Run the downloaded file and select the customized installation.  Select the ''Add Python 3.9 to PATH'' at the bottom.  Leave everything as is (press ''Next'' on the first screen), with the exception of the install location.  Set the install location as shown to ''C:\Python39''.

{{ :images:py39_win_setup.png?nolink&600 |}}

===== Downloading PyMOL ===== 

PyMOL is a complex bit of software, but someone has assembled it to work on Windows for us (thanks [[https://www.lfd.uci.edu/~gohlke/|Christoph Gohlke]]!).

  - From the [[https://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol|Pymol-open-source]] section on the Gohlke page, download the file ''pymol‑2.4.0‑cp39‑cp39‑win_amd64.whl'' in directory ''C:\pymol_installation''.  You need to create this directory first from Windows Explorer.
  - Under the same section, [[https://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol|PyMOL]], on the Gohlke page, also download the file ''pymol_launcher‑2.1‑cp39‑cp39‑win_amd64.whl'' in directory ''C:\pymol_installation''.

You should now have two files in your ''C:\pymol_installation'' directory.

===== Installing PyMOL (and its Dependencies) ===== 

  - Open a //Command Prompt//.  Search for the //Command Prompt//, right-click and click on //Run as administrator// option.
  - In the command prompt execute ''pip install wheel''.
  - Go to the PyMOL installation directory ''cd \pymol_installation''
  - Run the command ''pip install pymol‑2.3.0‑cp37‑cp37m‑win_amd64.whl''
  - Run the command ''pip install pymol_launcher‑2.1‑cp37‑cp37m‑win_amd64.whl''

===== Running PyMOL ===== 

To run PyMOL you just need to type ''pymol'' in the //Command Prompt//.  Alternatively, browse your ''C:\Python39\Scripts'' directory, right-click on the file ''pymol.exe'' and select the option //Send to// followed by //Desktop (create shortcut)//.  You can now access PyMOL by clicking on the PyMOL icon on your desktop.

Get in touch if you have any problems.