X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBCanvas.java;h=70f959fccad698f285e64e877d999487b762a778;hb=d406dae9bb29125d7a7017e4eb6e2e45ba47135b;hp=f853106f27be4997a05deef079c28d9ffd51c568;hpb=62387bf69fd0fb3fccb599213f7bd477d8bf383e;p=jalview.git

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index f853106..70f959f 100755
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -189,8 +189,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
         scale = findScale();
 
-
-        updateSeqColours();
         ToolTipManager.sharedInstance().registerComponent(this);
         ToolTipManager.sharedInstance().setInitialDelay(0);
         ToolTipManager.sharedInstance().setDismissDelay(10000);
@@ -215,6 +213,10 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
           }
         }
       }
+
+      updateSeqColours();
+      redrawneeded = true;
+      repaint();
     }
 
 
@@ -430,7 +432,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       {
         for (int ii = 0; ii < pdb.chains.size(); ii++)
         {
-          colourBySequence( mainchain );
+          colourBySequence( (PDBChain) pdb.chains.elementAt(ii));
         }
       }
 
@@ -478,6 +480,9 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         tmp.startCol = Color.lightGray;
         tmp.endCol = Color.lightGray;
 
+        if(chain!=mainchain)
+          continue;
+
         if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
             (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))
         {
@@ -513,8 +518,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
     public void drawScene(Graphics g)
     {
-
-
         if (zbuffer)
         {
             Zsort.Zsort(visiblebonds);
@@ -543,7 +546,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
                 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
                     g.setColor(tmpBond.startCol.darker().darker());
                     drawLine(g, xstart, ystart, xmid, ymid);
-
                     g.setColor(tmpBond.endCol.darker().darker());
                     drawLine(g, xmid, ymid, xend, yend);
                 } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
@@ -976,7 +978,5 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       mainchain.isVisible = true;
       findCentre();
       setupBonds();
-      redrawneeded = true;
-      repaint();
     }
 }