send rotCanvas sequence and viewport

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 3177bfc..aed4a33 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -589,14 +589,10 @@ public class PopupMenu extends JPopupMenu
       EBIFetchClient ebi = new EBIFetchClient();\r
       String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);\r
 \r
+      System.out.println("Got "+ sequence.getPDBId() );\r
       PDBfile pdb = new PDBfile(result);\r
-      sequence.setPDBfile(pdb);\r
 \r
-      ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).isVisible = true;\r
-      ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).sequence = sequence;\r
-    //  ( (PDBChain)pdb.chains.elementAt(sequence.maxchain)).colourBySequence();\r
-\r
-      rotCanvas rc = new rotCanvas(pdb);\r
+      rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);\r
       JInternalFrame frame = new JInternalFrame();\r
       frame.setContentPane(rc);\r
       Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);\r