Uploaded August 2023 | Updated September 2026, 1 hour ago

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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:
• proteopedia.org/wiki/index.php/CPK#:~:text=CPK%20Color%20Scheme%20for%20the,yellow%2C%20and%20hydrogen%20is%20white.
• PDB ID: 6PFK
• Schirmer, T., Evans, P. Structural basis of the allosteric behaviour of phosphofructokinase. Nature 343, 140–145 (1990). doi.org/10.1038/343140a0