a name="l00638"></a>00638 
<a name="l00639"></a>00639     <span class="comment">// Get a single transformation that moves the dbase site to the query</span>
<a name="l00640"></a>00640     A_model-&gt;get_current_inverse_3D_transform(&amp;(align-&gt;Q), align-&gt;T);
<a name="l00641"></a>00641     align-&gt;Q.get_ortho_rot_mat(align-&gt;R);
<a name="l00642"></a>00642     align-&gt;score = (align-&gt;score - <a class="code" href="classSimSite3D_1_1ScoreRigidAlignments.html#e2a77ac5a0d9b23d4149c04dde1e445d">A_