X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=c082463c2d762b3d09734d040106582b2a0ad4f9;hb=1efa38acf4e8102bf4e64b08005f8dc21bdd0145;hp=ad8b54cb023fa9204757b08fd83360b17b4ac4a9;hpb=3fb1cce1e733047ba3efa344690df45a1bd50452;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index ad8b54c..c082463 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -413,6 +413,7 @@ public synchronized void addSequence(SequenceI [] seq)
 
   public void seqColour_actionPerformed(ActionEvent actionEvent)
   {
+    lastCommand = null;
     colourBySequence = seqColour.isSelected();
     colourBySequence(ap.alignFrame.alignPanel);
   }
@@ -588,17 +589,13 @@ public synchronized void addSequence(SequenceI [] seq)
       resetLastRes.append(":" + chain);
     }
 
-    eval.append(";wireframe 100");//color gold;
+    eval.append(";wireframe 100;"+eval.toString()+".CA;");
 
-   // Color col = new Color(viewer.getAtomArgb(atomIndex));
+    resetLastRes.append(";wireframe 0;"+resetLastRes.toString()+".CA;spacefill 0;");
 
-    resetLastRes.append(";wireframe 0;select none;");//color["
-                       // + col.getRed() + ","
-                       // + col.getGreen() + ","
-                       // + col.getBlue() + "];
+    eval.append("spacefill 200;select none");
 
     viewer.evalStringQuiet(eval.toString());
-
   }
 
   public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
@@ -847,7 +844,8 @@ public synchronized void addSequence(SequenceI [] seq)
     if (chainId != null)
       picked+=(":"+chainId.substring(1, chainId.length()));
 
-    picked+=".C";
+    picked+=".CA";
+
 
     if (!atomsPicked.contains(picked))
     {