Also allow for some overlap to ensure loop closure. I.e.
proteinA aaaaaaaaaaaaaaaa---------aaaaaaaaaaaa proteinB -----------------------bbbbbbbbbbb---------------- sequence cccccccccccccccccccccccccccccccccc
On 7 May 2012 16:21, Thomas Evangelidis tevang3@gmail.com wrote:
> 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 >> > > > > -- > > ====================================================================== > > Thomas Evangelidis > > PhD student > > Biomedical Research Foundation, Academy of Athens > > 4 Soranou Ephessiou , 115 27 Athens, Greece > > email: tevang@bioacademy.gr > > tevang3@gmail.com > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > >