Sorry, my question is much more elementary. I see an example from the tutorial (Advanced Modeling, Modeling ligands in the binding site) on an alignment similar to what I want. However, I don't see the associated script to give this alignment, only the resulting pap file. In this example, only the binding pocket of the 1emd structure was included in the alignment. I would also need to know how not to include a region in one of the other sequences. Thanks.
On May 7, 2012, at 9:43 AM, Thomas Evangelidis wrote:
> 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/ > > > > > > -- > ====================================================================== > 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/ > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage