Have you ever tried to represent your protein as a “sausage”-style cartoon, with the tube diameter scaled by values in the B-factor column ? We present an array of useful PyMOL scripts links to solve your problem.
PyMOL scripts collection: http://rosettadesigngroup.com/blog/?p=10

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Rosetta Design Group
http://rosettadesigngroup.com
http://rosettadesigngroup.com/blog/