On 07/06/2011 07:40 AM, Chugunov Anton wrote:
What I expect, is a single-chain model that consists of four domains, each built from respective template's chain according to the alignment. What I get (as far as I see from the *.ini file, since no models output due to high energy-function) is the first domain followed by a huge non-structured loop
If the alignment you posted is the one you're actually using, then you have aligned DOM 2 through 4 with gaps in your template, so obviously Modeller has no structure to work with in that region. Remove all of those gaps from your template so that DOM-2 is aligned with BBBB, DOM-3 with CCCC and DOM-4 with DDDD.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage