code: public boolean checkScaleMatrix(Matrix4d scaleMatrix) {
  
  		Matrix3d mtranspose = getMTranspose();
  		for (int i=0;i<3;i++) {
  			for (int j=0;j<3;j++) {
  				if (!deltaComp(mtranspose.getElement(i, j),scaleMatrix.getElement(i, j))) {
  					//System.out.println("Our value   ("+i+","+j+"): "+getM().getElement(i,j));
  					//System.out.println("Their value ("+i+","+j+"): "+scaleMatrix.getElement(i,j));
  					return false;
  				}
  			}
  		}
  		for (int i=0;i<3;i++) {
  			if (!deltaComp(scaleMatrix.getElement(i, 3),0)) {
  				return false;
  			}
  		}
  		return true;
  	}
docs: Given a scale matrix parsed from a PDB entry (SCALE1,2,3 records),
  compares it to our calculated Mtranspose matrix to see if they coincide and
  returns true if they do.
  If they don't that means that the PDB entry is not in the standard
  orthogonalisation (NCODE=1 in ccp4).
  In 2011's remediation only 148 PDB entries were found not to be in
  a non-standard orthogonalisation. See:
  http://www.wwpdb.org/documentation/2011remediation_overview-061711.pdf
  For normal cases the scale matrix is diagonal without a translation component.
  Additionally the translation component of the SCALE matrix is also checked to
  make sure it is (0,0,0), if not false is return
  @param scaleMatrix
  @return