X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=9d06aef88ff0dfd78a57460e1f76dfa5e0d70740;hb=77ac7f545e96bd4bde47991f77291a71eb5b90e6;hp=6bc8f8485809b1d3e6d7f7b172122a6d744986c3;hpb=25217bbd06c4435ad995fd8ddf3620c3b1d68cd3;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 6bc8f84..9d06aef 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -607,17 +607,18 @@ public class StructureSelectionManager
     HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
     int resNum = -10000;
     int index = 0;
+    char insCode = ' ';
 
     do
     {
       Atom tmp = maxChain.atoms.elementAt(index);
-      if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
+      if ((resNum != tmp.resNumber || insCode != tmp.insCode)
+              && tmp.alignmentMapping != -1)
       {
         resNum = tmp.resNumber;
+        insCode = tmp.insCode;
         if (tmp.alignmentMapping >= -1)
         {
-          // TODO (JAL-1836) address root cause: negative residue no in PDB
-          // file
           mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber,
               tmp.atomIndex });
         }