Thank you to Pavel, Robbie and Mark og tak til Bjørn og Robert.
It was the last day of this student's project and she was doing some kind of coarse-grain protein dynamics model. This was the first time she asked me for help so I had to both (try) to understand what she was doing and figure out how to help her in the quickest manner while introducing the fewest new pieces of software. And I was a bit tired *ahem* from the going away party the night before.
Robbie's solution was by far the easiest. Basically, he has a list of all the Wilson B-factors for experimental data in the pdb from his work on PDB_REDO. It's a long list.
This gave her more consistent data when analysing the experimental structures. I don't know if it measurably influenced the model results.
The lesson is of course that if you are going to analyse data deposited by other people... Blah, blah. Starting over.
If you analyse x-ray crystal structures and you aren't a crystallographer then you should go ally yourself with one from the beginning.
Thanks for all the help and suggestions guys.
-Morten