PyMOL 101, Lesson 5: Select by Distance, the Mouse Control Menu, and Labeling

In this lesson, KP will show you how to generate a binding site quickly, by creating a selection sphere within a certain number of angstroms from a bound ligand. This lesson focuses on the mouse control menu, and how to use edit mode to reposition labels. 00:00 Intro 00:26 Setting up your workspace 01:57 The mouse control menu 02:34 Selected by distance from a ligand 03:41 Adjusting water sphere size 04:09 Find polar contacts (display binding site interactions) 04:46 Modifying the binding site residue selection 05:50 Show only the amino acid side chains 06:25 Labeling the binding site residues 06:44 Edit mode and moving labels 07:41 Display the binding site without cartoon REFERENCES • PDB ID: 6PFK • Schirmer, T., Evans, P. Structural basis of the allosteric behaviour of phosphofructokinase. Nature 343, 140–145 (1990). https://doi.org/10.1038/343140a0