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

Zhiqiang Ye wrote:
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.
That particular patch only affects TOP scripts, so won't change the results you got with Python. (It won't change the results with TOP scripts either, unless you were trying to use the RENAME_SEGMENTS command.) 


     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?
No; objective function values from different restraint sets (as you'll get for different size proteins) are not comparable. 

	Ben Webb, Modeller Caretaker
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