[modeller_usage] About the topini.patch for 8v2 and the energy

Dear all,

I have two questions about modeller.

The first one is about the patch file topini.patch for 8v2 (http://salilab.org/modeller/wiki/Patches). Before the patching, I have run many modelling jobs with error message, do I need to rerun the jobs after the patching? I used python scripts to do my modelling job, not TOP scripts.

The second question is the model.energy(). Can I compare the energy values between proteins of different size? If not, can I normalize them so that I can compare them?

Thank you very much!

-- Zhiqiang Ye