From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 25 Nov 2005 17:56:20 +0000 (+0000)
Subject: Read in Hetatms, allow for models, highlight in canvas
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=001bbb88f11b8a6cb2fb67aa30a64fe15ae454fb;p=jalview.git

Read in Hetatms, allow for models, highlight in canvas
---

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 0815dc0..6ae2baa 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -20,8 +20,6 @@ package MCview;
 
 import java.awt.*;
 
-import java.util.*;
-
 
 public class Atom {
     float x;
@@ -39,7 +37,7 @@ public class Atom {
 
     public Atom(String str)
     {
-        name =  str.substring(12,16);
+        name =  str.substring(12,15).trim();
 
         resName = str.substring(17,20);
 
@@ -50,6 +48,7 @@ public class Atom {
         this.x = (float) (new Float(str.substring(30,38).trim()).floatValue());
         this.y = (float) (new Float(str.substring(38,46).trim()).floatValue());
         this.z = (float) (new Float(str.substring(47,55).trim()).floatValue());
+
     }
 
     public void setColor(Color col) {
diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index 5ff0f1f..b3eb23f 100755
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -66,33 +66,29 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
     int xmid;
     int ymid;
     Font font = new Font("Helvetica", Font.PLAIN, 10);
-    jalview.gui.SequenceRenderer sr;
-    jalview.gui.FeatureRenderer  fr;
     jalview.gui.SeqCanvas seqcanvas;
     public Sequence sequence;
     final StringBuffer mappingDetails = new StringBuffer();
     PDBChain mainchain;
+    Vector highlightRes;
+    boolean pdbAction = false;
 
     public PDBCanvas(jalview.gui.SeqCanvas seqcanvas, Sequence seq)
     {
       this.seqcanvas = seqcanvas;
       this.sequence = seq;
-      sr = seqcanvas.getSequenceRenderer();
-      fr = seqcanvas.getFeatureRenderer();
-
       seqcanvas.setPDBCanvas(this);
     }
 
   public void setPDBFile(PDBfile pdb)
    {
-        this.sr = sr;
-        this.fr = fr;
         int max = -10;
         int maxchain = -1;
         int pdbstart = 0;
         int pdbend = 0;
         int seqstart = 0;
         int seqend = 0;
+        int [] mapping = null;
 
         for (int i = 0; i < pdb.chains.size(); i++)
         {
@@ -120,14 +116,17 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
             as.printAlignment(ps);
 
-            if (as.maxscore > max) {
+
+
+            if (as.maxscore > max)
+            {
                 max = as.maxscore;
                 maxchain = i;
-
                 pdbstart = as.seq2start;
                 pdbend = as.seq2end;
                 seqstart = as.seq1start + sequence.getStart()-1;
                 seqend = as.seq1end + sequence.getEnd()-1;
+                mapping = as.getExactMapping();
             }
 
             mappingDetails.append("\nPDB start/end "  + pdbstart + " " + pdbend);
@@ -141,9 +140,10 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         mainchain.seqstart = seqstart;
         mainchain.seqend = seqend;
         mainchain.isVisible = true;
-        mainchain.sequence = sequence;
+        mainchain.seqMapping = mapping;
+      //  mainchain.sequence = sequence;
 
-        this.pdb = pdb;
+      this.pdb = pdb;
         this.prefsize = new Dimension(getWidth(), getHeight());
 
         //Initialize the matrices to identity
@@ -195,6 +195,8 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         findCentre();
         findWidth();
 
+        setupBonds();
+
         scale = findScale();
 
 
@@ -202,10 +204,29 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         ToolTipManager.sharedInstance().registerComponent(this);
         ToolTipManager.sharedInstance().setInitialDelay(0);
         ToolTipManager.sharedInstance().setDismissDelay(10000);
+    }
+
+    Vector visiblebonds;
+    void setupBonds()
+    {
+      // Sort the bonds by z coord
+      visiblebonds = new Vector();
+
+      for (int ii = 0; ii < pdb.chains.size(); ii++)
+      {
+        if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
+        {
+          Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
 
+          for (int i = 0; i < tmp.size(); i++)
+          {
+            visiblebonds.addElement(tmp.elementAt(i));
+          }
+        }
+      }
     }
 
-    public void deleteBonds() {
+   public void deleteBonds() {
         scale = 0;
         maxwidth = 0;
 
@@ -367,8 +388,8 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         centre[2] = ztot / (2 * (float) bsize);
     }
 
-    public void paintComponent(Graphics g) {
-
+    public void paintComponent(Graphics g)
+    {
       super.paintComponent(g);
 
       if(pdb==null)
@@ -382,8 +403,11 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
         //Only create the image at the beginning -
         //this saves much memory usage
-        if ((img == null) || (prefsize.width != getWidth()) ||
-                (prefsize.height != getHeight())) {
+        if ((img == null)
+            || (prefsize.width != getWidth())
+            || (prefsize.height != getHeight()))
+
+      {
             prefsize.width = getWidth();
             prefsize.height = getHeight();
 
@@ -395,7 +419,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
             ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
                                  RenderingHints.VALUE_ANTIALIAS_ON);
 
-
             redrawneeded = true;
         }
 
@@ -407,6 +430,8 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         }
 
         g.drawImage(img, 0, 0, this);
+
+        pdbAction = false;
     }
 
     public void drawAll(Graphics g, int width, int height)
@@ -420,6 +445,12 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
     public void updateSeqColours()
     {
+      if(pdbAction)
+      {
+        return;
+      }
+
+     // System.out.println("update seq colours");
       if(bysequence && pdb!=null)
       {
         for (int ii = 0; ii < pdb.chains.size(); ii++)
@@ -430,77 +461,69 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
       redrawneeded=true;
       repaint();
-
     }
 
     // This method has been taken out of PDBChain to allow
     // Applet and Application specific sequence renderers to be used
     void colourBySequence(PDBChain chain)
     {
+     // System.out.println("colour by seq");
       for (int i = 0; i < chain.bonds.size(); i++)
       {
         Bond tmp = (Bond) chain.bonds.elementAt(i);
+        tmp.startCol = Color.lightGray;
+        tmp.endCol = Color.lightGray;
 
         if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
             (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))
         {
-          int pos = chain.seqstart +
-              (tmp.at1.resNumber - chain.pdbstart - chain.offset);
-
-          int index = sequence.findIndex(pos);
 
-          tmp.startCol = sr.findSequenceColour(Color.lightGray, sequence, index);
+          int pos = // chain.seqstart + Don't include seqstart here, start from 0
+              (tmp.at1.resNumber - chain.pdbstart - chain.offset)+1;
 
-          tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);
+            int index = chain.seqMapping[pos];
+            if (index != -1)
+            {
+              tmp.startCol = seqcanvas.getSequenceRenderer().findSequenceColour(
+                  Color.lightGray, sequence, index);
 
-        }
-        else
-        {
-          tmp.startCol = Color.gray;
+              tmp.startCol = seqcanvas.getFeatureRenderer().findFeatureColour(tmp.
+                  startCol, sequence, index);
+            }
         }
 
         if ( (tmp.at2.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
             (tmp.at2.resNumber <= ( (chain.pdbend + chain.offset) - 1)))
         {
-          int pos = chain.seqstart +
-              (tmp.at2.resNumber - chain.pdbstart - chain.offset);
-          int index = sequence.findIndex(pos);
+          int pos = // chain.seqstart + Don't include seqstart here, start from 0
+              (tmp.at2.resNumber - chain.pdbstart - chain.offset)+1;
 
-          tmp.endCol = sr.findSequenceColour(tmp.endCol, sequence, index);
-          tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index);
-        }
-        else
-        {
-          tmp.endCol = Color.gray;
+            int index = chain.seqMapping[pos];
+            if (index != -1)
+            {
+              tmp.endCol = seqcanvas.getSequenceRenderer().findSequenceColour(
+                  tmp.endCol, sequence, index);
+              tmp.endCol = seqcanvas.getFeatureRenderer().findFeatureColour(tmp.
+                  endCol, sequence, index);
+            }
         }
       }
     }
 
 
-    public void drawScene(Graphics g) {
-        // Sort the bonds by z coord
-        Vector bonds = new Vector();
-
-        for (int ii = 0; ii < pdb.chains.size(); ii++)
-        {
-          if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
-          {
-            Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+    public void drawScene(Graphics g)
+    {
 
-            for (int i = 0; i < tmp.size(); i++)
-            {
-              bonds.addElement(tmp.elementAt(i));
-            }
-          }
-        }
 
-        if (zbuffer) {
-            Zsort.Zsort(bonds);
+        if (zbuffer)
+        {
+            Zsort.Zsort(visiblebonds);
         }
 
         Bond tmpBond=null;
-        for (int i = 0; i < bonds.size(); i++) {
-            tmpBond = (Bond) bonds.elementAt(i);
+        for (int i = 0; i < visiblebonds.size(); i++)
+        {
+            tmpBond = (Bond) visiblebonds.elementAt(i);
 
             xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) +
                 (getWidth() / 2));
@@ -515,7 +538,8 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
             xmid = (xend + xstart) / 2;
             ymid = (yend + ystart) / 2;
 
-            if (depthcue && !bymolecule) {
+            if (depthcue && !bymolecule)
+            {
                 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
                     g.setColor(tmpBond.startCol.darker().darker());
                     drawLine(g, xstart, ystart, xmid, ymid);
@@ -613,13 +637,37 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       }
     }
 
-    public void mousePressed(MouseEvent e) {
+    public void mousePressed(MouseEvent e)
+    {
+        pdbAction = true;
         Atom fatom = findAtom(e.getX(), e.getY());
         if(fatom!=null)
         {
           fatom.isSelected = !fatom.isSelected;
+
           redrawneeded = true;
           repaint();
+          if (foundchain != -1)
+          {
+            PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);
+            if (chain == mainchain)
+            {
+              int pos = // chain.seqstart + Don't include seqstart here, start from 0
+                  (fatom.resNumber - chain.pdbstart - chain.offset) +1 ;
+
+              if (chain.seqMapping[pos] != -1)
+              {
+                if (highlightRes == null)
+                  highlightRes = new Vector();
+
+                if (highlightRes.contains((chain.seqMapping[pos]) + ""))
+                  highlightRes.remove((chain.seqMapping[pos]) + "");
+                else
+                  highlightRes.add((chain.seqMapping[pos]) + "");
+              }
+            }
+          }
+
         }
         mx = e.getX();
         my = e.getY();
@@ -628,7 +676,16 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         dragging = false;
     }
 
-    public void mouseMoved(MouseEvent e) {
+    public void mouseMoved(MouseEvent e)
+    {
+      pdbAction = true;
+      if(highlightBond1!=null)
+      {
+        highlightBond1.at2.isSelected = false;
+        highlightBond2.at1.isSelected = false;
+        highlightBond1 = null;
+        highlightBond2 = null;
+      }
 
         Atom fatom = findAtom(e.getX(), e.getY());
 
@@ -638,43 +695,72 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
           chain = (PDBChain) pdb.chains.elementAt(foundchain);
           if(chain == mainchain)
           {
-            int pos = chain.seqstart +
-                (fatom.resNumber - chain.pdbstart - chain.offset) + 1;
-
-            int index = seqcanvas.getViewport().getAlignment().findIndex(
-                sequence);
+           int pos = // chain.seqstart + Don't include seqstart here, start from 0
+               (fatom.resNumber - chain.pdbstart - chain.offset) +1 ;
 
-            seqcanvas.highlightSearchResults(new int[]
-                                             {index, pos, pos});
+            highlightSeqcanvas( chain.seqMapping[pos] );
           }
         }
-        else
-          seqcanvas.highlightSearchResults(null);
 
         if (fatom != null)
         {
             this.setToolTipText(chain.id+":"+ fatom.resNumber+" "+ fatom.resName);
         } else
         {
-            this.setToolTipText("");
+            highlightSeqcanvas( -1);
+            this.setToolTipText(null);
         }
     }
 
-    public void mouseClicked(MouseEvent e) {
-    }
 
-    public void mouseEntered(MouseEvent e) {
-    }
+    void highlightSeqcanvas(int pos)
+    {
+      int index = seqcanvas.getViewport().getAlignment().findIndex(sequence);
 
-    public void mouseExited(MouseEvent e) {
+      int size = pos==-1?0:3;
+
+      if(highlightRes!=null)
+        size += highlightRes.size()*3;
+
+      int [] array = new int[size];
+      int i=0;
+      if(highlightRes!=null)
+      {
+        for (i = 0; i < highlightRes.size(); i++)
+        {
+          int a = Integer.parseInt(highlightRes.elementAt(
+              i).toString())+1;
+          array[i * 3] = index;
+          array[ (i * 3) + 1] = a;
+          array[ (i * 3) + 2] = a;
+        }
+      }
+
+      if(pos!=-1)
+      {
+        array[i * 3] = index;
+        array[i * 3 + 1] = pos+1;
+        array[i * 3 + 2] = pos+1;
+      }
+
+      seqcanvas.highlightSearchResults(array);
     }
 
-    public void mouseDragged(MouseEvent evt) {
+
+    public void mouseClicked(MouseEvent e)  { }
+
+    public void mouseEntered(MouseEvent e) {  }
+
+    public void mouseExited(MouseEvent e) { }
+
+    public void mouseDragged(MouseEvent evt)
+    {
         int x = evt.getX();
         int y = evt.getY();
         mx = x;
         my = y;
 
+
         MCMatrix objmat = new MCMatrix(3, 3);
         objmat.setIdentity();
 
@@ -716,7 +802,8 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         repaint();
     }
 
-    public void mouseReleased(MouseEvent evt) {
+    public void mouseReleased(MouseEvent evt)
+    {
         dragging = false;
         return;
     }
@@ -729,20 +816,17 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
             if (chain.isVisible)
             {
-                Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
-                for (int i = 0; i < bonds.size(); i++)
+                for (int i = 0; i < chain.bonds.size(); i++)
                 {
-                    Bond tmpBond = (Bond) bonds.elementAt(i);
+                    Bond tmpBond = (Bond) chain.bonds.elementAt(i);
 
                     if (tmpBond.at1.isSelected)
                     {
                         labelAtom(g, tmpBond, 1);
                     }
-
-                    if (tmpBond.at2.isSelected)
+                    else if (tmpBond.at2.isSelected)
                     {
-
                         labelAtom(g, tmpBond, 2);
                     }
                 }
@@ -752,14 +836,14 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
     public void labelAtom(Graphics g, Bond b, int n) {
         g.setFont(font);
-
-        if (n == 1) {
+        g.setColor(Color.red);
+        if (n == 1)
+        {
             int xstart = (int) (((b.start[0] - centre[0]) * scale) +
                 (getWidth() / 2));
             int ystart = (int) (((b.start[1] - centre[1]) * scale) +
                 (getHeight() / 2));
 
-            g.setColor(Color.red);
             g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
         }
 
@@ -769,7 +853,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
             int ystart = (int) (((b.end[1] - centre[1]) * scale) +
                 (getHeight() / 2));
 
-            g.setColor(Color.red);
             g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
         }
     }
@@ -841,12 +924,28 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
     }
 
    Bond highlightBond1, highlightBond2;
+   String alignMouseOver;
    public void highlightRes(int ii)
   {
+
+    int index = ii - mainchain.seqstart;
+
+    if (highlightRes!=null
+        && highlightRes.contains( mainchain.seqMapping[index]+ ""))
+    {
+       return;
+    }
+
+    if(highlightBond1!=null)
+      highlightBond1.at2.isSelected = false;
+
+    if(highlightBond2!=null)
+      highlightBond2.at1.isSelected = false;
+
     highlightBond1 = null;
     highlightBond2 = null;
 
-    int index = ii - mainchain.seqstart;
+
 
     if(index <0 )
       return;
@@ -856,10 +955,16 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       if(index>0)
       {
         highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
+        highlightBond1.at2.isSelected = true;
+       // highlightBond1.at2.isSelected = true;
       }
 
       if(index!=mainchain.bonds.size())
+      {
         highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
+        highlightBond2.at1.isSelected = true;
+     //   highlightBond2.at2.isSelected = true;
+      }
     }
 
     redrawneeded = true;
@@ -875,5 +980,8 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       }
       mainchain.isVisible = true;
       findCentre();
+      setupBonds();
+      redrawneeded = true;
+      repaint();
     }
 }
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 43c8e9d..3cf73d1 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -39,6 +39,7 @@ public class PDBChain {
     public int pdbend = 0;
     public int seqstart = 0;
     public int seqend = 0;
+    public int [] seqMapping;
 
     //public DrawableSequence ds;
     public PDBChain(String id) {
@@ -57,15 +58,19 @@ public class PDBChain {
         return tmp;
     }
 
-    public void makeCaBondList() {
-        for (int i = 0; i < (residues.size() - 1); i++) {
+    public void makeCaBondList()
+    {
+        for (int i = 0; i < (residues.size() - 1); i++)
+        {
             Residue tmpres = (Residue) residues.elementAt(i);
             Residue tmpres2 = (Residue) residues.elementAt(i + 1);
             Atom at1 = tmpres.findAtom("CA");
             Atom at2 = tmpres2.findAtom("CA");
 
-            if ((at1 != null) && (at2 != null)) {
-                if (at1.chain.equals(at2.chain)) {
+            if ((at1 != null) && (at2 != null))
+            {
+                if (at1.chain.equals(at2.chain))
+                {
                     makeBond(at1, at2);
                 }
             }
@@ -89,11 +94,12 @@ public class PDBChain {
 
     public void makeResidueList() {
         int count = 0;
-        String seq = "";
+        StringBuffer seq = new StringBuffer();
 
-        for (int i = 0; i < atoms.size(); i++) {
+        int i, iSize = atoms.size()-1;
+        for (i = 0; i < iSize; i++)
+        {
             Atom tmp = (Atom) atoms.elementAt(i);
-            //String resName = tmp.resName;
             int resNumber = tmp.resNumber;
             int res = resNumber;
 
@@ -131,21 +137,23 @@ public class PDBChain {
             Atom tmpat = (Atom) tmpres.atoms.elementAt(0);
 
             // Keep totting up the sequence
-            if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null) {
-                System.err.println("PDBReader:Null aa3Hash for " +
-                    tmpat.resName);
+            if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null)
+            {
+                seq.append("X") ;
+               //  System.err.println("PDBReader:Null aa3Hash for " +
+               //     tmpat.resName);
             } else {
-                String tmpres2 = ResidueProperties.aa[((Integer) ResidueProperties.getAA3Hash()
-                                                                                  .get(tmpat.resName)).intValue()];
-                seq = seq + tmpres2;
+
+                seq.append(ResidueProperties.aa[((Integer) ResidueProperties.getAA3Hash()
+                                                                                  .get(tmpat.resName)).intValue()]);
             }
         }
 
         if(id.length()<1 || id.equals(" "))
            id = "_";
 
-        sequence = new Sequence(id, seq, 1, seq.length());
-     //   System.out.println("PDB Sequence is :\nSequence = " + seq);
+        sequence = new Sequence(id, seq.toString(), 1, seq.length());
+      //  System.out.println("PDB Sequence is :\nSequence = " + seq);
      //   System.out.println("No of residues = " + residues.size());
     }
 
diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index 06b6f65..082ce6e 100755
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -19,9 +19,13 @@ public class PDBViewer extends JInternalFrame implements Runnable
                    Sequence seq,
                    SeqCanvas seqcanvas)
   {
+
     pdb = entry;
     sequence = seq;
 
+    Thread worker = new Thread(this);
+    worker.start();
+
     try
     {
       jbInit();
@@ -42,10 +46,8 @@ public class PDBViewer extends JInternalFrame implements Runnable
       title.append( " Chain:" );
       title.append( pdb.getProperty().get("chains"));
     }
-    Desktop.addInternalFrame(this,title.toString(),400, 400);
 
-     Thread worker = new Thread(this);
-     worker.start();
+     Desktop.addInternalFrame(this,title.toString(),400, 400);
   }
 
   public void run()
@@ -53,8 +55,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
     try
     {
       EBIFetchClient ebi = new EBIFetchClient();
-      String[] result = ebi.fetchData("pdb:" + pdb.getId(), null,
-                                      null);
+      String[] result = ebi.fetchData("pdb:" + pdb.getId(), "default","raw");
 
       PDBfile pdbfile = new PDBfile(result);
 
@@ -337,7 +338,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   public void mapping_actionPerformed(ActionEvent e)
   {
     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
-    Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 500, 600);
+    Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
     cap.setText(pdbcanvas.mappingDetails.toString());
   }
 
diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 2b22b24..c4fe563 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -71,7 +71,9 @@ public class PDBfile extends jalview.io.FileParse {
 
     public void parse()
     {
+        PDBChain tmpchain;
         String line;
+        boolean modelFlag = false;
         for (int i = 0; i < lineArray.size(); i++)
         {
 
@@ -83,16 +85,29 @@ public class PDBfile extends jalview.io.FileParse {
              continue;
            }
 
-                if (line.indexOf("ATOM") == 0) {
+           if(line.indexOf("MODEL")==0)
+             modelFlag = true;
+
+           if(modelFlag && line.indexOf("ENDMDL")==0)
+             break;
+
+           if (line.indexOf("ATOM")==0 || line.indexOf("HETATM")==0 )
+            {
                     try {
                         Atom tmpatom = new Atom(line);
 
-                        if (findChain(tmpatom.chain) != null)
+                        //Jalview is only interested in CA bonds????
+                        if(!tmpatom.name.equals("CA"))
+                          continue;
+
+                        tmpchain = findChain(tmpatom.chain);
+                        if ( tmpchain != null)
                         {
-                            findChain(tmpatom.chain).atoms.addElement(tmpatom);
-                        } else
+                          tmpchain.atoms.addElement(tmpatom);
+                        }
+                        else
                         {
-                            PDBChain tmpchain = new PDBChain(tmpatom.chain);
+                            tmpchain = new PDBChain(tmpatom.chain);
                             chains.addElement(tmpchain);
                             tmpchain.atoms.addElement(tmpatom);
                         }
diff --git a/src/MCview/Residue.java b/src/MCview/Residue.java
index efaf1f0..0f24137 100755
--- a/src/MCview/Residue.java
+++ b/src/MCview/Residue.java
@@ -33,9 +33,12 @@ public class Residue {
         this.count = count;
     }
 
-    public Atom findAtom(String name) {
-        for (int i = 0; i < atoms.size(); i++) {
-            if (((Atom) atoms.elementAt(i)).name.equals(name)) {
+    public Atom findAtom(String name)
+    {
+        for (int i = 0; i < atoms.size(); i++)
+        {
+            if (((Atom) atoms.elementAt(i)).name.equals(name))
+            {
                 return (Atom) atoms.elementAt(i);
             }
         }