From 2a198f35d10d35bd4c3eef1b0f5e623252bfa564 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 30 Oct 2009 10:22:11 +0000
Subject: [PATCH] na pdb: detect P backbone

---
 src/MCview/PDBfile.java |   11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index b368b91..3df320c 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -64,8 +64,10 @@ public class PDBfile extends jalview.io.AlignFile
       String line;
       boolean modelFlag = false;
       boolean terFlag = false;
+      String lastID="";
 
       int index = 0;
+      String atomnam=null;
       while ((line = nextLine()) != null)
       {
         if (line.indexOf("HEADER") == 0)
@@ -110,7 +112,8 @@ public class PDBfile extends jalview.io.AlignFile
           terFlag = false;
 
           // Jalview is only interested in CA bonds????
-          if (!line.substring(12, 15).trim().equals("CA"))
+          atomnam = line.substring(12, 15).trim();
+          if (!atomnam.equals("CA") && !atomnam.equals("P"))
           {
             continue;
           }
@@ -119,6 +122,11 @@ public class PDBfile extends jalview.io.AlignFile
           tmpchain = findChain(tmpatom.chain);
           if (tmpchain != null)
           {
+            if (tmpatom.resNumIns.trim().equals(lastID))
+            {
+              //  phosphorylated protein - seen both CA and P..
+              continue;
+            }
             tmpchain.atoms.addElement(tmpatom);
           }
           else
@@ -127,6 +135,7 @@ public class PDBfile extends jalview.io.AlignFile
             chains.addElement(tmpchain);
             tmpchain.atoms.addElement(tmpatom);
           }
+          lastID = tmpatom.resNumIns.trim();
         }
         index++;
       }
-- 
1.7.10.2