X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2FMCview%2FAtom.java;h=0a3bd3988ed0fdb55b89d5ba64957cfc404d9452;hb=7f700a0a56fa9946b0186bffa34f510777599c66;hp=8b160efddbb8085ccbe27a942596599007053cf2;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 8b160ef..0a3bd39 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -50,9 +50,10 @@ public class Atom
   public int atomIndex;
 
   public float occupancy = 0;
-
+  
   public float tfactor = 0;
-
+  // need these if we ever want to export Atom data
+  // public boolean tfacset=true,occset=true;
   public boolean isSelected = false;
 
   public Atom(String str)
@@ -71,9 +72,22 @@ 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());
-    occupancy = (float) (new Float(str.substring(54, 60).trim())
-            .floatValue());
-    tfactor = (float) (new Float(str.substring(60, 66).trim()).floatValue());
+    // optional entries - see JAL-730
+    String tm = str.substring(54, 60).trim();
+    if (tm.length()>0) {
+      occupancy = (float) (new Float(tm)).floatValue();
+    } else {
+      occupancy = 1f; // default occupancy
+      // see note above: occset=false;
+    }
+    tm = str.substring(60, 66).trim();
+    if (tm.length()>0)
+    {
+      tfactor = (float) (new Float(tm).floatValue());
+    } else {
+      tfactor = 1f;
+      //see note above: tfacset=false;
+    }
   }
 
   public Atom(float x, float y, float z)