X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAtom.java;fp=src%2FMCview%2FAtom.java;h=68a7c21e53bf0244449e1096b4a4a33466031ecb;hb=9623cea766a766683243235557ad48e6f7659e6a;hp=4d000af30de2f23089bf045d5106b8bdcf60607d;hpb=6066400ed6b0fe288ebbea82389f59838a534706;p=jalview.git

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 4d000af..68a7c21 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -20,6 +20,8 @@
  */
 package MCview;
 
+import jalview.schemes.ResidueProperties;
+
 import java.awt.Color;
 
 public class Atom
@@ -73,11 +75,13 @@ public class Atom
     name = str.substring(12, 15).trim();
 
     resName = str.substring(17, 20);
+    // JAL-1828 treat MSE Selenomethionine as MET (etc)
+    resName = ResidueProperties.getCanonicalAminoAcid(resName);
 
     chain = str.substring(21, 22);
 
     resNumber = Integer.parseInt(str.substring(22, 26).trim());
-    resNumIns = str.substring(22, 27).trim();
+    resNumIns = str.substring(22, 27);
     insCode = str.substring(26, 27).charAt(0);
     this.x = (new Float(str.substring(30, 38).trim()).floatValue());
     this.y = (new Float(str.substring(38, 46).trim()).floatValue());