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Hallo Tânia, you can try 'Rapido' by R. Mosca and T. Schneider at EMBL Hamburg. It is available as a web application under: http://webapps.embl-hamburg.de/rapido/ Best wishes, Gerrit Langer. Tânia Oliveira wrote: > Hello, > > I´m having a problem that I would like to know if someone could help me. > > I want to do a 3D structure based alignment of my protein with another > one. The problem is that my protein has 2 domains, and the structure > that I want to superimpose just have one. I can do the structure > superimposition by hand, but I´m not being able to do the sequence > alignment based on the 3D structure, because the program that I´m > using (SSM) starts to superimpose the sequence of my second domain in > the beginning of the sequence of my reference model (exactly the same > thing that it does with the sequence of the first domain). > > Do you know if there is any program where I can do this. > > Thanks in advance, > > > > > > Tânia Oliveira, PhD Student > > Membrane Protein Crystallography and Microbial Biochemistry Laboratory > - ITQB-UNL > > >