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" ?