X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAssociatePdbFileWithSeq.java;fp=src%2Fjalview%2Fgui%2FAssociatePdbFileWithSeq.java;h=ce75821a3535dea439bf1dcef203e730aea0e8f1;hb=e248608bb20e000c17ddc79390d9c1f1f0470e4f;hp=01f1cb0f960c4ebbba0249e96c5704d743ac8e4e;hpb=e3b3d5e7a207edb43253bb598e1a2f88d1142689;p=jalview.git

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index 01f1cb0..ce75821 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -44,10 +44,12 @@ public class AssociatePdbFileWithSeq
           SequenceI sequence, boolean prompt)
   {
     PDBEntry entry = new PDBEntry();
+    MCview.PDBfile pdbfile = null;
     try
     {
-      MCview.PDBfile pdbfile = new MCview.PDBfile(choice, protocol);
-
+      // TODO JAL-674 extract secondary structure and transfer it to associated
+      // sequence
+      pdbfile = new MCview.PDBfile(false, false, choice, protocol);
       if (pdbfile.id == null)
       {
         String reply = null;