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? Thank you very much. Adriana
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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
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aesteves＠fcien.edu.uy -
Modeller Caretaker