Hi,

In case the Espript route that Daniel recommended doesn't work for whatever
reason, I have a Perl script that will replace B-factor values with scores
read-in from a separate text file.  Visit "http://mccammon.ucsd.edu/~cmura/
PyMOL/Examples/conservation" to download the script and see an example of its 
usage (image file "SequConserv_example_1l5x.png").  Here's a 3-step recipe for
using it in Unix/Linux with a sample input file (1L5X.pdb):

(1) Create a file containing sequence conservation scores, ranked as "ss" (super
    strong), "s" (strong), "m" (medium), "w" (weak), or simply blank.  An 
    example of this file format for 1L5X is in "1l5x_conserved_sites.txt", and 
    it's also described in the top part of the "map_conservation_to_B.pl" file.


(2) Use the map_conservation_to_B.pl script to modify the B-factor fields, using
    1L5X.pdb and 1l5x_conserved_sites.txt as input, and redirect the output to a 
    new file ("1L5X_scores.pdb"):

    $] ./map_conservation_to_B.pl  1L5X.pdb  1l5x_conserved_sites.txt \
	> 1L5X_scores.pdb


(3) To visualize the conservation scores in PyMOL: (i) load the new
    1L5X_scores.pdb file ["load 1L5X_scores.pdb, 1l5x"]; (ii) load Robert 
    Campbell's color_b.py module into PyMOL ["run color_b.py"]; (iii) use the 
    color_b() function, e.g.:

    $] color_b('1l5x',gradient='bmr',mode='ramp',nbins=10,sat=0.7, \
	value=0.8)

Good luck, 
Cameron