X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;fp=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=5ff2da4cc02e3ee049f862a0e6bdff07c67ab175;hb=c03aaae74c93db1c8fa0e95258bfbccfe1d3106d;hp=671c3254cb7455d6a77553957b4a4abe494028be;hpb=500bc57b2d6901ff09f6b1511289f85ba9dec823;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 671c325..5ff2da4 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -600,11 +600,15 @@ public class StructureSelectionManager
         setProgressBar(null);
         setProgressBar(MessageManager
                 .getString("status.obtaining_mapping_with_phyre2_template_alignment"));
+        String fastaFile = getPhyre2FastaFileFor(pdbFile);
         StructureMapping phyre2ModelMapping = new Phyre2Client(pdb)
-                .getStructureMapping(seq, pdbFile,
-                        getPhyre2FastaFileFor(pdbFile), " ");
-
+                .getStructureMapping(seq, pdbFile, fastaFile, " ");
         seqToStrucMapping.add(phyre2ModelMapping);
+        maxChain.makeExactMapping(maxAlignseq, seq);
+        maxChain.transferRESNUMFeatures(seq, null);
+        jalview.datamodel.Mapping sqmpping = maxAlignseq
+                .getMappingFromS1(false);
+        maxChain.transferResidueAnnotation(phyre2ModelMapping, sqmpping);
         ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
       }
       else