Have you tried it and didn't work? This is how the alignment should look like. Just remember to superimpose the two templates (A, B) so that the loop ends look "joined".
On 7 May 2012 16:14, EGY mp.2egy@gmail.com wrote:
> I searched the archives and could not find how to do what seems to be a > simple procedure. I have a sequence that has high homology with a published > X-ray structure A. A second state of the protein is defined by the > conformation of a conserved loop. A related protein B containing the > conserved loop is in the second state, albeit with lower homology. I would > like to model the sequence in the second state using the structure A as a > template, but using structure B to model the loop only. I believe I need an > alignment like this: > proteinA aaaaaaaaaaaaaaaa-------------------aaaaaaaaaaaa > proteinB ----------------------------bbbbbbbbbbb--------------------- > sequence cccccccccccccccccccccccccccccccccccccccccccccc > > I realize this is a very simple question. I've been going through the > manual and searching the archives and cannot figure out how to do it. Any > help will be much appreciated. > Thanks. > EGY > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >