"HPPNcolor_v1.pml" is a PyMOL script that colors residues based on Hydrophobicity/Polarity, Positive/Negative charge, and residues (Pro, Gly) with unique main-chain dihedral angles. It colors 20 different amino acid residues as shown below.
Yellow: Val, Ile, Leu, Phe, Tyr, Trp, Met
Cyan: Asn, Gln, Ser, Thr
Blue: His, Lys, Arg
Red: Asp, Glu
Green: Gly Cartoon
Orange: Pro
White: Cartoon and Ala
Yellow-green (lime): Cys
This coloring is used to visualize the presence of exposed hydrophobic and buried hydrophilic residues, the position of Gly and Pro, and the distribution of positive and negative charged residues.
# PyMOL command line
PyMOL> run /path/to/HPPNcolor_v1.pml
# Manual
menubar "File" ---> "Run Script..." ---> Select "HPPNcolor_v1.pml" ---> "Open"
Since the backbone of cartoon representation is forced to be white, if you want to change the color, please use the following command to unset "cartoon_color".
# PyMOL command line
PyMOL> unset cartoon_color
PyMOL> unset cartoon_color, (all)
