04.1 PyMOL

4. PyMOL

4.1 How to Install PyMOL

PyMOL is an open-source biomolecule viewer which can be used to view proteins and their ligands. PyMOL can be downloaded from the following link, which will take you to the PyMOL by Schrödinger website: https://pymol.org/2/

PyMOL has two versions available: the incentive version and the open-source version. As a student, we have access to both of them: we can apply for an academic licence to use the incentive version (but only for educational purposes) or we could use the open-source version of PyMOL directly (free, can be used for publication). The link for academic licence registration is here: https://pymol.org/edu/?q=educational/

Download PyMOL by clicking on the “download now” button, and then selecting the correct version for your operating system.

You can also download PyMOL from the following sources:

https://anaconda.org/psi4/pymol

https://omicx.cc/2019/05/26/install-pymol-windows/ 

or PyMOL source code from GitHub: https://github.com/schrodinger/pymol-open-source

After you have installed PyMOL open the programme and you should find something looking like this:

An activation window will also pop up, requesting you to browse licences, you can ignore this and close the window. PyMOL will display the red “no license file” warning and give you a trial period of 30 days. However, do not worry, after this period expires you will still be able to use PyMOL, the message will simply start reading “0 days remaining” as you can see above.