X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=7836d24404ddabe97c5e269b7c63564c5e57b4c5;hb=3f12f4932226512316ec113e600695150431fd0a;hp=2cb75591697a26426be772ec0a01577762de61e3;hpb=318e3baf6738dea7b20640bc3e46814bd566811c;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 2cb7559..7836d24 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -270,6 +270,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       // diff < 5 then mark as valid and update termination Atom
       if (chainTerMap.containsKey(curAtomChId))
       {
+        if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
+        {
+          return false;
+        }
         if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
         {
           chainTerMap.put(curAtomChId, curAtom);
@@ -281,6 +285,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     // atom with previously terminated chain encountered
     else if (chainTerMap.containsKey(curAtomChId))
     {
+      if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
+      {
+        return false;
+      }
       if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
       {
         chainTerMap.put(curAtomChId, curAtom);