X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=be042e6b6476a7491dc7494d89a138d6771662d9;hb=0f40a8334651302a74a223ecd3e583451302bb42;hp=33c566d2d1e68d5796b12639c5694d19b7ebd00a;hpb=cbf0b72e90f4c719dff345e467b5c9b9873247ed;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 33c566d..be042e6 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -385,7 +385,11 @@ public class StructureSelectionManager
     try
     {
 
-      if (pdbFile != null && isCIFFile(pdbFile))
+      boolean isParseWithJMOL = StructureImportSettings
+              .getDefaultPDBFileParser().equalsIgnoreCase(
+                      StructureImportSettings.StructureParser.JMOL_PARSER
+                              .toString());
+      if (isParseWithJMOL || (pdbFile != null && isCIFFile(pdbFile)))
       {
         pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
                 secStructServices, pdbFile, protocol);
@@ -501,7 +505,8 @@ public class StructureSelectionManager
       if (isMapUsingSIFTs)
       {
         setProgressBar(null);
-        setProgressBar("Obtaining mapping with SIFTS");
+        setProgressBar(MessageManager
+                .getString("status.obtaining_mapping_with_sifts"));
         jalview.datamodel.Mapping sqmpping = maxAlignseq
                 .getMappingFromS1(false);
         if (targetChainId != null && !targetChainId.trim().isEmpty())
@@ -559,7 +564,8 @@ public class StructureSelectionManager
       else
       {
         setProgressBar(null);
-        setProgressBar("Obtaining mapping with NW alignment");
+        setProgressBar(MessageManager
+                .getString("status.obtaining_mapping_with_nw_alignment"));
         seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
                 maxChain, pdb, maxAlignseq));
       }