X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;fp=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=cd986c0550cecca569f19e213f22cd26e3aacbbc;hb=df0734bbe3c42eb4e1d2e6471040888c85801ba5;hp=34ca6ba50c716ee020778855fb8356a725832d04;hpb=a7a69103cb81f7e40803cbed0beb41d05707f641;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 34ca6ba..cd986c0 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -399,7 +399,9 @@ public class StructureSelectionManager
       // FIXME if sourceType is not null, we've lost data here
       sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
       pdb = new JmolParser(false, pdbFile, sourceType);
-      pdb.addSettings(parseSecStr, parseSecStr, parseSecStr);
+      pdb.addSettings(parseSecStr && processSecondaryStructure,
+              parseSecStr && addTempFacAnnot,
+              parseSecStr && secStructServices);
       pdb.doParse();
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
               && DataSourceType.FILE == sourceType)