--- trunk/SHAPES/RigidBody.cpp	2004/06/22 18:04:58	1285
+++ trunk/SHAPES/RigidBody.cpp	2004/06/23 23:19:43	1292
@@ -318,6 +318,7 @@ void RigidBody::calcRefCoords( ) {
     pAxisMat[i][0] = sU[i][maxAxis];
   }
     
+  
   //calculate the proper rotation matrix
   transposeMat3(pAxisMat, pAxisRotMat);
   
@@ -330,6 +331,14 @@ void RigidBody::calcRefCoords( ) {
   
   identityMat3(iMat);
   setA(iMat);
+  
+  //and resort the moments of intertia to match the new orientation
+  for (i=0; i<3; i++)
+    if (evals[i]<momIntTol)
+      evals[i] = 0.0;
+  I[0][0] = evals[maxAxis];
+  I[1][1] = evals[midAxis];
+  I[2][2] = evals[pAxis];
 }
 
 void RigidBody::doEulerToRotMat(double euler[3], double myA[3][3] ){
@@ -536,3 +545,9 @@ double RigidBody::getAtomEps(int index){
   return myAtoms[index]->getEps();
   
 }
+
+char *RigidBody::getAtomBase(int index){
+  
+  return myAtoms[index]->getBase();
+  
+}