code: public void runOptimization(int maxi) throws StructureException{
  		superimposeBySet();
  		if ( debug)
  			System.err.println("   initial rmsd " + rmsd);
  
  //      if (showAlig)
  //         showCurrentAlignment(equLen, equSet, "after initial superimposeBySet Len:" +equLen + " rmsd:" +rmsd);
  
  		maxKeepStep = 4;
  		keepStep = 0;
  
  		optimize(maxi);
  	}
docs: run the optimization
  
  @param maxi maximum nr. of iterations
  @throws StructureException