X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=9e319c1f38e2b6d581c4c4b5626b22bb0c73615b;hb=6157950da0bf97e1fafa6b60ed95df21d9c609de;hp=4fffe6f101f54312cd7a839bcb8dca8e08c02244;hpb=173f77ac7161e8866ddfe6b5689d61a83f459cfc;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 4fffe6f..9e319c1 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -2295,6 +2295,7 @@ public class Jalview2XML
 
       jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
       af = loadJalviewAlign(jprovider);
+      af.setMenusForViewport();
 
     } catch (MalformedURLException e)
     {
@@ -4249,7 +4250,8 @@ public class Jalview2XML
       StructureData filedat = oldFiles.get(id);
       String pdbFile = filedat.getFilePath();
       SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
-      binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE);
+      binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
+              null);
       binding.addSequenceForStructFile(pdbFile, seq);
     }
     // and add the AlignmentPanel's reference to the view panel