JAL-2136 New Phyre2 branch + attempt to resynced with develop

[jalview.git] / src / jalview / structure / AtomSpec.java

diff --git a/src/jalview/structure/AtomSpec.java b/src/jalview/structure/AtomSpec.java
index f20cd31..54e2261 100644 (file)
--- a/src/jalview/structure/AtomSpec.java
+++ b/src/jalview/structure/AtomSpec.java
@@ -88,8 +88,12 @@ public class AtomSpec
       throw new IllegalArgumentException(spec);
     }
 
-    String chainId = dotPos == -1 ? "" : residueChain.substring(dotPos + 1);
-
+    String chainId = dotPos == -1 ? " " : residueChain
+            .substring(dotPos + 1);
+    if (chainId.length() == 0)
+    {
+      chainId = " ";
+    }
     return new AtomSpec(modelId, chainId, resNum, 0);
   }