X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=cd986c0550cecca569f19e213f22cd26e3aacbbc;hb=1dc67d212f52a92d7917fc9f4edd47d99b97c149;hp=ad259fd88d0e957830b429597a4c1209cad3f5f2;hpb=083fb85bfa1be57c30db0ac1cb9f5f8ad08d1060;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index ad259fd..cd986c0 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -398,8 +398,11 @@ public class StructureSelectionManager
     {
       // FIXME if sourceType is not null, we've lost data here
       sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
-      pdb = new JmolParser(pdbFile, sourceType);
-
+      pdb = new JmolParser(false, pdbFile, sourceType);
+      pdb.addSettings(parseSecStr && processSecondaryStructure,
+              parseSecStr && addTempFacAnnot,
+              parseSecStr && secStructServices);
+      pdb.doParse();
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
               && DataSourceType.FILE == sourceType)
       {