Preparing an input file for docking - 1st steps for PyRx input

Docking molecules in PyRx using Vina requires that you clean up the input target protein. You often need to start with a structure file, e.g. 5hnk.pdb which contains many molecules. The information in the file often provides clues to where you should target your docking. Here is an example of extracting just a single relevant protein chain for docking, saving it as a .pdb file ready for PyRx docking and also saving an annotated .pse file that show scenes with different representations showing the area you want to target for docking (which you "surround " with the docking box in PyRx just before running Vina. Using PyMOL first helps you to locate the region you want to target- the so-called "druggable pocket".