JAL-2136 New Phyre2 branch + attempt to resynced with develop

[jalview.git] / src / MCview / PDBCanvas.java

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index 83642cc..f25b431 100644 (file)
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -153,7 +153,8 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
     try
     {
-      pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
+      pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol,
+              ap.alignFrame);
 
       if (protocol.equals(jalview.io.DataSourceType.PASTE))
       {