X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=9ecf630b571a4b54639c3378e8308a16f1d561a8;hb=f9062df1303c1ff071075256cf4b7ad7c9db9658;hp=336c6f84d1a1e9529a6715c1d93ba4298bae2cf6;hpb=0b6e9403e96ee9f0d41211b2f90130ff850c4e98;p=jalview.git

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 336c6f8..9ecf630 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -61,6 +61,7 @@ import jalview.structure.AtomSpec;
 import jalview.structure.AtomSpecModel;
 import jalview.structure.StructureCommandI;
 import jalview.structure.StructureCommandsI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
 import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
@@ -925,7 +926,7 @@ public abstract class AAStructureBindingModel
       // todo better way to ensure synchronous than setting getReply true!!
       executeCommands(commandGenerator.showBackbone(), true, null);
       
-      boolean isNucleotide = structures[refStructure].isRna;
+      AtomSpecType backbone = structures[refStructure].isRna ? AtomSpecType.PHOSPHATE : AtomSpecType.ALPHA;
       /*
        * superpose each (other) structure to the reference in turn
        */
@@ -935,7 +936,7 @@ public abstract class AAStructureBindingModel
         {
           AtomSpecModel atomSpec = getAtomSpec(structures[i], matched);
           List<StructureCommandI> commands = commandGenerator
-                  .superposeStructures(refAtoms, atomSpec,isNucleotide);
+                  .superposeStructures(refAtoms, atomSpec, backbone);
           List<String> replies = executeCommands(commands, true, null);
           for (String reply : replies)
           {