X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;fp=src%2Fjalview%2Fbin%2FCommands.java;h=c8489085e3f8772835cdc441048eaa719f053448;hp=e01d40acb22462298ea342dd0798e893bb8ad460;hb=69827911885f6e7ed824b5e6f2f802e0a23c25f0;hpb=546cce1523d08c53ffdc744d46907cf8c98bdc10

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index e01d40a..c848908 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -328,9 +328,17 @@ public class Commands
           }
 
           // colour alignment
-          String colour = avm.getFromSubValArgOrPref(av, Arg.COLOUR, sv,
-                  null, "DEFAULT_COLOUR_PROT", "");
-          this.colourAlignFrame(af, colour);
+          String colour = null;
+          if (avm.containsArg(Arg.COLOUR)
+                  || !(format == FileFormat.Jalview))
+          {
+            colour = avm.getFromSubValArgOrPref(av, Arg.COLOUR, sv, null,
+                    "DEFAULT_COLOUR_PROT", null);
+          }
+          if (colour != null)
+          {
+            this.colourAlignFrame(af, colour);
+          }
 
           // Change alignment frame title
           String title = avm.getFromSubValArgOrPref(av, Arg.TITLE, sv, null,