Python, Windows and PyMol

So I was chatting with an ex-colleague who had been having some fun getting PyMol to install on Windows. So I thought I’d do a quick write-up.

To start with, you need four things:

  1. The latest (C)Python installation package (AMD64 for 64-bit Windows 10)
  2. The NumPy+MKL wheel from Christoph Gohlke’s collection for AMD64
  3. The PyMol wheel from the same for AMD64
  4. The PyMol Launcher wheel from the same (optional) for AMD64

Install Python:

Make sure to tick “add to path” also, disable the pathlength limit, since it’s an option:

Open a commandline: (shift+right click)

Use pip to install wheel:

Then install NumPy+MKL:

Then PyMol: (this will also pull in Pmw)

Then PyMol Launcher (if you want)

Then find where PyMol is installed: (a ‘cheat’ here is %appdata% in the address bar!)

And create a shortcut on the Desktop/Start Menu/Task Bar (to your taste)…

Protein loaded is 5XA7, a recent submission and nothing whatsoever to do with me. I just picked it for demonstration purposes.

And now it should work! In all honesty, I find the pip install system far more trouble than just finding and installing the relevant libraries used to be…

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