04.6 How to Use the PyMOL Command Line

4.6 How to Use the PyMOL Command Line

By now you will already be familiar with the basic logic of PyMOL and should be confident with performing a lot of manipulations to your proteins structure. PyMOL has a lot of functionality which can be easily accessed from the graphical user interface (i.e. clicking and selecting things using the side menu). Whilst this way of using PyMOL is visually intuitive and quick to learn, it can sometimes be time consuming doing everything manually step-by-step. The command line offers a faster way of performing many actions in PyMOL and offers users a way to create custom scripts which quickly transform the way a protein is visualised.

The crystal structure selected for this tutorial is 3uag (MurD ligase from E. Coli crystallised with two substrates called UMA and ADP). As the UMA binding site can be viewed as a potential target site, this tutorial is going to teach you how to use command line to visualise the interactions at the UMA active site and produce a publication-quality image of it in PyMOL.

Useful links:

The PyMOL command reference library:

https://pymol.org/pymol-command-ref.html

The PyMOL script library:

https://pymolwiki.org/index.php/Category:Script_Library