add a simple sample

doc/samples/index.rst

@@ -3,5 +3,6 @@ List of PV samples
 
 .. toctree::
 
+  structure-with-ligand
   ensemble/index
   hover/index

doc/samples/structure-with-ligand.rst

@@ -0,0 +1,33 @@
+Display protein together with ligands
+========================================
+
+This sample shows how to render a protein in cartoon mode and display the contained ligands as balls-and-sticks. For this particular example, we have chosen the dengue methyl transferase structure (1r6a) which contains a s-adenosyl homocysteine and the inhibitor ribavirin 5' triphosphate.
+
+
+.. pv-sample:: 
+
+  <script>
+  var parent = document.getElementById('viewer');
+  var viewer = pv.Viewer(parent,
+                        { width : 300, height : 300, antialias : true });
+  pv.io.fetchPdb('http://www.rcsb.org/pdb/files/1r6a.pdb', function(structure) {
+    // select the two ligands contained in the methyl transferase by name, so
+    // we can display them as balls and sticks.
+    viewer.on('viewerReady', function() {
+      var ligand = structure.select({rnames : ['RVP', 'SAH']});
+      viewer.ballsAndSticks('ligand', ligand);
+      // display the whole protein as cartoon
+      viewer.cartoon('protein', structure);
+
+      // set camera orientation to pre-determined rotation, zoom and
+      // center values that are optimal for this very protein
+      var rotation = [
+        0.1728139370679855, 0.1443438231945038,  0.974320650100708,
+        0.0990324765443802, 0.9816440939903259, -0.162993982434272,
+        -0.9799638390541077, 0.1246569454669952,  0.155347332358360
+      ];
+      var center = [6.514, -45.571, 2.929];
+      viewer.setCamera(rotation, center, 73);
+    });
+  });
+  </script>