X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=65504e4bdebcfec7077acedced1811dd6700c6a9;hb=723d0cff35b408c12fc13b44ff50193c588d6ff1;hp=d5597de1480381f412e2e42d2e8bfb0302bab44f;hpb=cbb5b519ea1986d0e2016a6472e7583ec98c5294;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index d5597de..65504e4 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -99,7 +99,7 @@ public class PDBChain
   /**
    * Annotate the residues with their corresponding positions in s1 using the
    * alignment in as
-   * 
+   * NOTE: This clears all atom.alignmentMapping values on the structure.
    * @param as
    * @param s1
    */
@@ -107,7 +107,11 @@ public class PDBChain
   {
     int pdbpos = as.getSeq2Start() - 2;
     int alignpos = s1.getStart() + as.getSeq1Start() - 3;
-
+    // first clear out any old alignmentMapping values:
+    for (Atom atom: (Vector<Atom>) atoms) { 
+      atom.alignmentMapping=-1;
+    }
+    // and now trace the alignment onto the atom set.
     for (int i = 0; i < as.astr1.length(); i++)
     {
       if (as.astr1.charAt(i) != '-')