This little script will color the surface of your protein the same color as the b-factors from the alpha carbons of each amino acid. This script is useful when you want to color a protein by the b-factor column, but all you have in the b-factor for each alpha carbon. If you try to color a surface based only on the alpha carbon b-factors, then the surface isn't rendered as you typically want.
# in PyMOL type the following
# fetch 1cll
fetch 1cll
# load your b-factor column; for "1cll" you can simulate fake data
# by writing 144 random integers to /tmp/bb. If you have some real
# data, then put that there. 1 row for each alpha carbon.
f = open('/tmp/bb', 'r').readlines();
# alter the alpha carbon coords
alter *,b=0
alter n. CA, b=f.pop(0)
# color the surface
e2s 1cll
