PyMOL 101, Lesson 4: Color, Transparency, and Alternate Renderings

In this installment of PyMOL 101, KP talks about CPK coloring and color settings in PyMOL. We’ll learn to change renderings, color them, and apply transparency. 00:00 Intro AND CPK coloring 00:40 Phosphofructokinase background 01:24 Setting up your workspace 02:06 Color by chain 03:23 Color by secondary structure 03:52 Surface transparency 04:51 Color by element 06:05 Terminology break 06:28 Rendering a ligand 07:26 Cartoon transparency 08:14 Overview of the different renderings REFERENCES: • https://proteopedia.org/wiki/index.ph.... • 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