simran jeet wrote: > I have generated models for proteins but dont know how to optimize and > refine those structures using modellar. I have tried using the > optimize.py file to optimize with CG but i am not able to understand the > script and where should I list the protein name to be optimized in that > script file.

Models generated using the automodel class have already been optimized and refined, although you may want to try some loop refinement: http://salilab.org/modeller/9v2/manual/node34.html

I can't really give you any specific help with the "optimize.py" script unless you can ask more specific questions. What script are you referring to, and what don't you understand about it?

Ben Webb, Modeller Caretaker