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 is, as defined on its home page: “.. a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation”. Indeed it is one of the most popular molecular viewers out there. One of the main strengths of PyMOL is its inherent scripting abilities. I’m sure that many of you knew that, but have never really taken the time to write such scripts, and why would you ? others have done the job for you!