Can we superimpose more than 2 structures in biojava?

Question

[Janeeta Raja]

Is there any way to do multiple alignment of structures in biojava or convert multiple alignment to pdb file?

[roy.granit]

Have you considered using PyMol?

[andreas.prlic]

Check out the MultipleAlignmentGUI class in Biojava. It allows to create a multiple structure alignment.