diff --git src/jalview/schemes/ClustalxColourScheme.java src/jalview/schemes/ClustalxColourScheme.java
old mode 100755
new mode 100644
index 92d2dd7..544f26c
--- src/jalview/schemes/ClustalxColourScheme.java
+++ src/jalview/schemes/ClustalxColourScheme.java
@@ -1,357 +1,365 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3
  * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License
  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
+import jalview.util.MessageManager;
 
 import java.awt.Color;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
 import java.util.Vector;
+
+import javax.swing.JOptionPane;
 
 public class ClustalxColourScheme extends ResidueColourScheme // implements
 // IParameterizable
 {
   public static Hashtable colhash = new Hashtable();
 
   Hashtable[] cons;
 
   int[][] cons2;
 
   ConsensusColour[] colours;
 
   ConsensusColour[] ResidueColour;
 
   int size;
 
   Consensus[] conses = new Consensus[32];
 
   Vector colourTable = new Vector();
 
   private boolean includeGaps = true;
 
   {
     colhash.put("RED", new Color((float) 0.9, (float) 0.2, (float) 0.1));
     colhash.put("BLUE", new Color((float) 0.5, (float) 0.7, (float) 0.9));
     colhash.put("GREEN", new Color((float) 0.1, (float) 0.8, (float) 0.1));
     colhash.put("ORANGE", new Color((float) 0.9, (float) 0.6, (float) 0.3));
     colhash.put("CYAN", new Color((float) 0.1, (float) 0.7, (float) 0.7));
     colhash.put("PINK", new Color((float) 0.9, (float) 0.5, (float) 0.5));
     colhash.put("MAGENTA", new Color((float) 0.8, (float) 0.3, (float) 0.8));
     colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
   }
 
   public ClustalxColourScheme(AnnotatedCollectionI alignment,
           Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
     alignmentChanged(alignment, hiddenReps);
   }
 
   public void alignmentChanged(AnnotatedCollectionI alignment,
           Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
     int maxWidth = alignment.getWidth();
-    List<SequenceI> seqs = alignment.getSequences(hiddenReps);
-    cons2 = new int[maxWidth][24];
-    includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
-    // get the current setting of the
-    // includeGaps param.
-    int start = 0;
-
-    // Initialize the array
-    for (int j = 0; j < 24; j++)
-    {
-      for (int i = 0; i < maxWidth; i++)
-      {
-        cons2[i][j] = 0;
-      }
+    if (maxWidth>0){
+	    List<SequenceI> seqs = alignment.getSequences(hiddenReps);
+	    cons2 = new int[maxWidth][24];
+	    includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
+	    // get the current setting of the
+	    // includeGaps param.
+	    int start = 0;
+	
+	    // Initialize the array
+	    for (int j = 0; j < 24; j++)
+	    {
+	      for (int i = 0; i < maxWidth; i++)
+	      {
+	        cons2[i][j] = 0;
+	      }
+	    }
+	
+	    int res;
+	    int i;
+	    int j = 0;
+	    char[] seq;
+	
+	    for (SequenceI sq : seqs)
+	    {
+	      seq = sq.getSequence();
+	
+	      int end_j = seq.length - 1;
+	
+	      for (i = start; i <= end_j; i++)
+	      {
+	        if ((seq.length - 1) < i)
+	        {
+	          res = 23;
+	        }
+	        else
+	        {
+	          res = ResidueProperties.aaIndex[seq[i]];
+	        }
+	
+	        cons2[i][res]++;
+	      }
+	
+	      j++;
+	    }
+	
+	    this.size = seqs.size();
+	    makeColours();
+    }else{
+        JOptionPane.showMessageDialog(Desktop.desktop, "Error","Error",JOptionPane.WARNING_MESSAGE);    	
     }
-
-    int res;
-    int i;
-    int j = 0;
-    char[] seq;
-
-    for (SequenceI sq : seqs)
-    {
-      seq = sq.getSequence();
-
-      int end_j = seq.length - 1;
-
-      for (i = start; i <= end_j; i++)
-      {
-        if ((seq.length - 1) < i)
-        {
-          res = 23;
-        }
-        else
-        {
-          res = ResidueProperties.aaIndex[seq[i]];
-        }
-
-        cons2[i][res]++;
-      }
-
-      j++;
-    }
-
-    this.size = seqs.size();
-    makeColours();
   }
 
   public void makeColours()
   {
     conses[0] = new Consensus("WLVIMAFCYHP", 60);
     conses[1] = new Consensus("WLVIMAFCYHP", 80);
     conses[2] = new Consensus("ED", 50);
     conses[3] = new Consensus("KR", 60);
     conses[4] = new Consensus("G", 50);
     conses[5] = new Consensus("N", 50);
     conses[6] = new Consensus("QE", 50);
     conses[7] = new Consensus("P", 50);
     conses[8] = new Consensus("TS", 50);
 
     conses[26] = new Consensus("A", 85);
     conses[27] = new Consensus("C", 85);
     conses[10] = new Consensus("E", 85);
     conses[11] = new Consensus("F", 85);
     conses[12] = new Consensus("G", 85);
     conses[13] = new Consensus("H", 85);
     conses[14] = new Consensus("I", 85);
     conses[15] = new Consensus("L", 85);
     conses[16] = new Consensus("M", 85);
     conses[17] = new Consensus("N", 85);
     conses[18] = new Consensus("P", 85);
     conses[19] = new Consensus("Q", 85);
     conses[20] = new Consensus("R", 85);
     conses[21] = new Consensus("S", 85);
     conses[22] = new Consensus("T", 85);
     conses[23] = new Consensus("V", 85);
     conses[24] = new Consensus("W", 85);
     conses[25] = new Consensus("Y", 85);
     conses[28] = new Consensus("K", 85);
     conses[29] = new Consensus("D", 85);
 
     conses[30] = new Consensus("G", 0);
     conses[31] = new Consensus("P", 0);
 
     // We now construct the colours
     colours = new ConsensusColour[11];
 
     Consensus[] tmp8 = new Consensus[1];
     tmp8[0] = conses[30]; // G
     colours[7] = new ConsensusColour((Color) colhash.get("ORANGE"), tmp8);
 
     Consensus[] tmp9 = new Consensus[1];
     tmp9[0] = conses[31]; // P
     colours[8] = new ConsensusColour((Color) colhash.get("YELLOW"), tmp9);
 
     Consensus[] tmp10 = new Consensus[1];
     tmp10[0] = conses[27]; // C
     colours[9] = new ConsensusColour((Color) colhash.get("PINK"), tmp8);
 
     Consensus[] tmp1 = new Consensus[14];
     tmp1[0] = conses[0]; // %
     tmp1[1] = conses[1]; // #
     tmp1[2] = conses[26]; // A
     tmp1[3] = conses[27]; // C
     tmp1[4] = conses[11]; // F
     tmp1[5] = conses[13]; // H
     tmp1[6] = conses[14]; // I
     tmp1[7] = conses[15]; // L
     tmp1[8] = conses[16]; // M
     tmp1[9] = conses[23]; // V
     tmp1[10] = conses[24]; // W
     tmp1[11] = conses[25]; // Y
     tmp1[12] = conses[18]; // P
     tmp1[13] = conses[19]; // p
     colours[0] = new ConsensusColour((Color) colhash.get("BLUE"), tmp1);
 
     colours[10] = new ConsensusColour((Color) colhash.get("CYAN"), tmp1);
 
     Consensus[] tmp2 = new Consensus[5];
     tmp2[0] = conses[8]; // t
     tmp2[1] = conses[21]; // S
     tmp2[2] = conses[22]; // T
     tmp2[3] = conses[0]; // %
     tmp2[4] = conses[1]; // #
     colours[1] = new ConsensusColour((Color) colhash.get("GREEN"), tmp2);
 
     Consensus[] tmp3 = new Consensus[3];
 
     tmp3[0] = conses[17]; // N
     tmp3[1] = conses[29]; // D
     tmp3[2] = conses[5]; // n
     colours[2] = new ConsensusColour((Color) colhash.get("GREEN"), tmp3);
 
     Consensus[] tmp4 = new Consensus[6];
     tmp4[0] = conses[6]; // q = QE
     tmp4[1] = conses[19]; // Q
     tmp4[2] = conses[22]; // E
     tmp4[3] = conses[3]; // +
     tmp4[4] = conses[28]; // K
     tmp4[5] = conses[20]; // R
     colours[3] = new ConsensusColour((Color) colhash.get("GREEN"), tmp4);
 
     Consensus[] tmp5 = new Consensus[4];
     tmp5[0] = conses[3]; // +
     tmp5[1] = conses[28]; // K
     tmp5[2] = conses[20]; // R
     tmp5[3] = conses[19]; // Q
     colours[4] = new ConsensusColour((Color) colhash.get("RED"), tmp5);
 
     Consensus[] tmp6 = new Consensus[6];
     tmp6[0] = conses[3]; // -
     tmp6[1] = conses[29]; // D
     tmp6[2] = conses[10]; // E
     tmp6[3] = conses[6]; // QE
     tmp6[4] = conses[19]; // Q
     tmp6[5] = conses[2]; // DE
     colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);
 
     Consensus[] tmp7 = new Consensus[5];
     tmp7[0] = conses[3]; // -
     tmp7[1] = conses[29]; // D
     tmp7[2] = conses[10]; // E
     tmp7[3] = conses[17]; // N
     tmp7[4] = conses[2]; // DE
     colours[6] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp7);
 
     // Now attach the ConsensusColours to the residue letters
     ResidueColour = new ConsensusColour[20];
     ResidueColour[0] = colours[0]; // A
     ResidueColour[1] = colours[4]; // R
     ResidueColour[2] = colours[2]; // N
     ResidueColour[3] = colours[6]; // D
     ResidueColour[4] = colours[0]; // C
     ResidueColour[5] = colours[3]; // Q
     ResidueColour[6] = colours[5]; // E
     ResidueColour[7] = colours[7]; // G
     ResidueColour[8] = colours[10]; // H
     ResidueColour[9] = colours[0]; // I
     ResidueColour[10] = colours[0]; // L
     ResidueColour[11] = colours[4]; // K
     ResidueColour[12] = colours[0]; // M
     ResidueColour[13] = colours[0]; // F
     ResidueColour[14] = colours[8]; // P
     ResidueColour[15] = colours[1]; // S
     ResidueColour[16] = colours[1]; // T
     ResidueColour[17] = colours[0]; // W
     ResidueColour[18] = colours[10]; // Y
     ResidueColour[19] = colours[0]; // V
   }
 
   @Override
   public Color findColour(char c)
   {
     return Color.pink;
   }
 
   @Override
   public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour;
 
     if (cons2.length <= j
             || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
     {
       return Color.white;
     }
 
     int i = ResidueProperties.aaIndex[c];
 
     currentColour = Color.white;
 
     if (i > 19)
     {
       return currentColour;
     }
 
     for (int k = 0; k < ResidueColour[i].conses.length; k++)
     {
       if (ResidueColour[i].conses[k].isConserved(cons2, j, size,
               includeGaps))
       {
         currentColour = ResidueColour[i].c;
       }
     }
 
     if (i == 4)
     {
       if (conses[27].isConserved(cons2, j, size, includeGaps))
       {
         currentColour = (Color) colhash.get("PINK");
       }
     }
 
     if (conservationColouring)
     {
       currentColour = applyConservation(currentColour, j);
     }
 
     return currentColour;
   }
 
   /**
    * @return the includeGaps
    */
   protected boolean isIncludeGaps()
   {
     return includeGaps;
   }
 
   /**
    * @param includeGaps
    *          the includeGaps to set
    */
   protected void setIncludeGaps(boolean includeGaps)
   {
     this.includeGaps = includeGaps;
   }
 
   @Override
   public ColourSchemeI applyTo(AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     ClustalxColourScheme css = new ClustalxColourScheme(sg,
             hiddenRepSequences);
     css.includeGaps = includeGaps;
     return css;
   }
 }
 
 class ConsensusColour
 {
   Consensus[] conses;
 
   Color c;
 
   public ConsensusColour(Color c, Consensus[] conses)
   {
     this.conses = conses;
 
     // this.list = list;
     this.c = c;
   }
 }