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Re: [modeller_usage] Fwd: validation and log file

aesteves@fcien.edu.uy wrote:

I still worried about validation. I know I have to read the
model-default.log file to look for: objetive function and chose the
one with the lowest(I did it; the DOPE pseudo-energy value and de
value of GA341, and finally the restraint violations, but I did not
find the  third value and I dont know how to read violations. Can
anybody help me to read the log file and find the information I need
to validate my model?

Modeller will not calculate the GA341 energy by default - you have to
ask for it with 'assess.ga341' in your automodel script. Violations are less useful, but as a rule of thumb any violations of distance restraints greater than 3 standard deviations are probably an indication of a poor model. 
	Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org             http://www.salilab.org/modeller/
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