X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBCanvas.java;h=ee556a3a105c55b6cc59424b0ca01d2756619857;hb=77c35fa912621cbadcf5ec74da4c6d45de6322e1;hp=7da2705942224eaa6ff1c2269881d49092b89f8b;hpb=13b72a19a32edf45b82976ad2984c5ca3e40f37d;p=jalview.git

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index 7da2705..ee556a3 100755
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -449,10 +449,10 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
     int findTrueIndex(int pos)
     {
       // returns the alignment position for a residue
-      int j = 1; // first position in PDB atom coordinate sequence
+      int j = sequence.getStart(); // first position in PDB atom coordinate sequence
       int i = 0;
 
-      while ( (i < sequence.getLength()) && (j <= pos+1)) 
+      while ( (i < sequence.getLength()) && (j <= pos+1))
       {
         if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))
         {