On 3/21/14, 12:45 AM, Abhijit Muley wrote: > I am having knots in my structure, same problem as this person had- > http://salilab.org/archives/modeller_usage/2005/msg00394.html

If you're really modeling long loops similar to the original poster, you'll see from my response there that you're unlikely to be able to recover from that problem.

> I went through the manual but could not find any specific part where > such instructions have been mentioned (althought they could have been in > some section I have missed).

You'd have to dig into the Python code for the loopmodel class, subclass and override the method, and provide your own implementation. Definitely outside the scope of the manual, and let me reiterate that it's entirely possible it won't work anyway.

Ben Webb, Modeller Caretaker