Hi, sorry for a probable trivial question, but I couldn't find a solution browsing the mailing list by myself.
I want to model a protein using two different templates, in particular they differ in the position of a loop. My protein is very similar to template 1, but should have that loop in the same conformation found in template 2. So I'd like to "say" to modeller: please model my protein using template 1 as much as possible, but use only template 2 to model that loop. Please take in mind that both templates cover the entire sequence and show the loop (in different conformations). I tried to do this by replacing the residues that I would like to be discarded (in correspondence of the loop) in template 1 with gaps in the alignment. So for example:
target: AAAAAAAAAAAAAAAAA template 1: BBBB-------BBBBBB template 2: ZZZZZZZZZZZZZZZZZ (the part with gaps in template 1 is present in PDB file)
But Modeller returned me an error saying: Sequence difference between alignment and PDB: Alignment: BBBBBBBBBB Sequence: BBBBBBBBBBBBBBBBB
I understand that Modeller "interpret" my alignment as a gap would present in the structure, and since this is not the case, it returns me an error. The question is: how to correctly send information to Modeller in order to "force" it to follow only a template to model a portion of the sequence, even if the other template is present? It seems to me that there was a way to do it without modifying the PDB file of the first template in order to cancel this loop. Am I correct? Is there a solution? Thank you very much for kind assistance and best regards Anna
____________________________________________________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabotti@isa.cnr.it Skype account: annam1972 Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
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