Three files: sc.pdb, bb.pdb, and h2o.pdb - representing the side-chain, backbone, and h2o SSI, respectively.

# Visualize the b-factors in cartoon putty mode
PyMOL>cartoon putty

# Set the b-factor heatmap color
PyMOL>spectrum b, white_blue_green_yellow, minimum=0, maximum=1

# Show sticks for side chains with b-factor value above b=0.3
PyMOL>show sticks, sc & b>0.3

# To aid with visual clarity, turn on side-chain helper (i.e. hide backbone sticks)
PyMOL>set cartoon_side_chain_helper, on, sc

# Hide spheres for h2o pockets with b-factor value below b=0.3
PyMOL>hide spheres, h2o & b<0.3

# Hide the cartoon putty for side-chain SSI
PyMOL>set cartoon_transparency, 1, sc

# Ray trace the image
PyMOL>ray

# Save ray traced image as .png
PyMOL>png /path/to/directory/filename.png

