diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 89ef6f1dcabce2c64103eababff0f01b3e945608..c47c2504c62b1763e292d64c82593ad66bf15123 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -2748,6 +2748,8 @@ public class BamView extends JPanel
       if(!isStrandStackView())
         jspView.getVerticalScrollBar().setValue(
             jspView.getVerticalScrollBar().getMaximum());
+      else
+        setViewportMidPoint();
       showBaseAlignment = false;
       baseQualityColour.setEnabled(false);
       markInsertions.setEnabled(false);