public String toPDB(Structure s1, Structure s2){


		Structure newpdb = getAlignedStructure(s1, s2);

		return newpdb.toPDB();
	}
public String toPDB ( Structure s1 , Structure s2 ) { Structure newpdb = getAlignedStructure ( s1 , s2 ) ; return newpdb . toPDB ( ) ; }
converts the alignment to a PDB file
each of the structures will be represented as a model.


@param s1
@param s2
@return a PDB file as a String