_1ScoreRigidAlignments.html#896fa695aef8944e5a685ba3ef552b0c">A_max_num_aligns</a>, <a class="code" href="classSimSite3D_1_1ScoreRigidAlignments.html#7806e9477e19018757ac9095212e1263">A_score_cutoff</a>, 
<a name="l00333"></a>00333            A_fine_tune_tier2_alignments, dset_site);
<a name="l00334"></a>00334     }
<a name="l00335"></a>00335 
<a name="l00336"></a>00336     <span class="comment">// If we wanted only to fine tune the best scoring alignment, do it here</span>
<a name="l00337"></a>00337     <s