On 5/7/10 7:42 PM, Harish Reddy wrote: > I need some help with optimization. I am confused what to do.
Your best option is to build more models, assess them, and choose the best one (or change your alignment/template if none of the models are acceptable). You would be better off doing this with Python scripts, as the old Modeller TOP scripts are no longer documented or supported.
> On the first instance i used the scrip one to build the models. As i was > not satisfied with the structural quality of the models, i used the > second script below where i included a refinement command. Even then i > couldn't get good models. So, i tried to a optimization script (third)
Actually, all your scripts do the same thing - they call the regular modeling procedure. You have changed the amount of refinement and the optimization parameters slightly, but this does not usually have a large influence on the output models.
> But that > script just kept on failing. So, I am not sure what the problem is..
I can't tell what the problem is either! What do you mean by "the script just kept on failing" ?
Ben Webb, Modeller Caretaker