code: public static void shiftCA2(AFPChain afpChain, Atom[] ca2,  Matrix m, Atom shift, Group[] twistedGroups) {
  
  		int i = -1;
  		for (Atom a: ca2){
  			i++;
  			Group g = a.getGroup();
  
  			Calc.rotate(g,m);
  			Calc.shift(g, shift);
  
  			if (g.hasAltLoc()){
  				for (Group alt: g.getAltLocs()){
  					for (Atom alta : alt.getAtoms()){
  						if ( g.getAtoms().contains(alta))
  							continue;
  						Calc.rotate(alta,m);
  						Calc.shift(alta,shift);
  					}
  				}
  			}
  			twistedGroups[i]=g;
  		}
  	}
docs: only shift CA positions.