@@ -38,7 +38,6 @@ public class BasePairParameters {
 
     private static Logger log = LoggerFactory.getLogger(BasePairParameters.class);
 
-
     // See URL http://ndbserver.rutgers.edu/ndbmodule/archives/reports/tsukuba/Table1.html
     // and the paper cited at the top of this class (also as Table 1).
     // These are hard-coded to avoid problems with resource paths.
@@ -406,8 +405,7 @@ public List<Chain> getNucleicChains(boolean removeDups) {
      * sequences and the canonical base pairs of DNA or RNA. Use MismatchedBasePairParameters
      * or TertiaryBasePairParameters for finding higher-order associations.
      * @param chains The list of chains already found to be nucleic acids
-     * @return The list of corresponding Watson-Crick groups as pairs, element 0 is on the
-     *  forward strand and element 1 is on the reverse strand.
+     * @return The list of corresponding Watson-Crick groups as pairs, as a Pair of nucleic acid Groups
      */
     public List<Pair<Group>> findPairs(List<Chain> chains) {
         List<Pair<Group>> result = new ArrayList<>();
@@ -448,7 +446,7 @@ public List<Pair<Group>> findPairs(List<Chain> chains) {
                     double distance = Math.sqrt(dx*dx+dy*dy+dz*dz);
                     //log.info("C8-C6 Distance (Å): " + distance);
                     // could be a base pair
-                    if (Math.abs(distance-10.0) < 5.0) {
+                    if (Math.abs(distance-10.0) < 4.0) {
                         boolean valid = true;
                         for (String atomname : ringMap.get(type1)) {
                             Atom a = g1.getAtom(atomname);
 
@@ -20,7 +20,8 @@
  */
 public class MismatchedBasePairParameters extends BasePairParameters {
 
-    protected static final double MaxStagger = 2.0, MaxShear = 5.0, MaxStretch = 5.0,
+    // These are the criteria used to select proper base pairs.
+    protected static double MaxStagger = 2.0, MaxShear = 5.0, MaxStretch = 5.0,
             MaxPropeller = 60.0;
 
     public MismatchedBasePairParameters(Structure structure, boolean RNA, boolean removeDups, boolean canonical) {
@@ -32,7 +33,7 @@ public MismatchedBasePairParameters(Structure structure, boolean RNA, boolean re
     /**
      * This is an implementation for finding non-canonical base pairs when there may be missing or overhanging bases.
      * @param chains The list of chains already found to be nucleic acids
-     * @return The list of the atom groups (residues) that are pairs, a Group[2] array
+     * @return The list of the atom groups (residues) that are pairs, as a Pair of nucleic acid Groups
      */
     @Override
     public List<Pair<Group>> findPairs(List<Chain> chains) {
@@ -59,7 +60,7 @@ public List<Pair<Group>> findPairs(List<Chain> chains) {
                         Atom a2 = g2.getAtom("C1'");
                         if (a1 == null || a2 == null) continue;
                         // C1'-C1' distance is one useful criteria
-                        if (Math.abs(a1.getCoordsAsPoint3d().distance(a2.getCoordsAsPoint3d()) - 10.0) > 3.0) continue;
+                        if (Math.abs(a1.getCoordsAsPoint3d().distance(a2.getCoordsAsPoint3d()) - 10.0) > 4.0) continue;
                         Pair<Group> ga = new Pair<>(g1, g2);
                         Matrix4d data = basePairReferenceFrame(ga);
                         // if the stagger is greater than 2 Å, it's not really paired.
 
@@ -21,17 +21,19 @@
  */
 public class TertiaryBasePairParameters extends BasePairParameters {
 
-    protected static final double MaxStagger = 2.0, MaxPropeller = 60.0;
+    // These are the criteria used to select proper base pairs.
+    protected static double MaxStagger = 2.0, MaxPropeller = 60.0;
 
     public TertiaryBasePairParameters(Structure structure, boolean RNA, boolean removeDups) {
         super(structure, RNA, removeDups);
     }
 
     /**
      * This is an alternative implementation of findPair() that looks for anything that would fit the
-     * criteria for a base-pair, useful for the context of tertiary structure of RNA.
+     * criteria for a base-pair, useful for the context of tertiary structure of RNA.  Intra-strand base pairs
+     * are found with this algorithm.
      * @param chains The list of chains already found to be nucleic acids
-     * @return
+     * @return A list of the Pair of groups that match the base pair criteria, including intra-strand groups.
      */
     @Override
     public List<Pair<Group>> findPairs(List<Chain> chains) {
@@ -53,7 +55,7 @@ public List<Pair<Group>> findPairs(List<Chain> chains) {
                     Atom a2 = g2.getAtom("C1'");
                     if (a1 == null || a2 == null) continue;
                     // C1'-C1' distance is one useful criteria
-                    if (Math.abs(a1.getCoordsAsPoint3d().distance(a2.getCoordsAsPoint3d())-10.0) > 5.0) continue;
+                    if (Math.abs(a1.getCoordsAsPoint3d().distance(a2.getCoordsAsPoint3d())-10.0) > 4.0) continue;
                     Pair<Group> ga = new Pair<>(g1, g2);
                     Matrix4d data = basePairReferenceFrame(ga);
                     // if the stagger is greater than 2 Å, it's not really paired.
 
@@ -72,7 +72,6 @@ public void testBasePair() throws IOException, StructureException {
         assertEquals(steps[4][5], 3.491, 0.02);
 
 
-
         structure = StructureIO.getStructure("1P71");
 
         bp = new MismatchedBasePairParameters(structure, false, false, false).analyze();