On Fri, Nov 19, 2004 at 11:28:15AM +0900, Han Choe wrote: > Let's say that I have two pdb files of protein A and protein B and that > approximate interactions of the two proteins are known. Then can I get a > complex structure using MODELLER by restraining the distances of two or > three interactions between A and B in the top file with the following type > of alignment file? > > >P1;A > structureX:A > --AAAAA--/------------* > >P1;B > structureX:B > -------------/--BBBBB--* > >P1;AB > sequence:AB > --AAAAA--/--BBBBB--* Sure, something like that should work. The quality of the final model will be very dependent on the number and type of A-B restraints you define, however, and you may need so many restraints that the optimization time becomes prohibitive. Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mailing list: http://salilab.org/mailman/listinfo/modeller_usage