X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=12bb21d9b82fabea7edbee953c12ebfd92579b0a;hb=55deb271c9f6fa106548013a9790db38d518cf6c;hp=6c934c801451cf8a8c72364670dbc3428424aa25;hpb=e7bad5b433c747aed96a6ec44fac18051d8b2476;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 6c934c8..12bb21d 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -26,6 +26,7 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.structures.models.AAStructureBindingModel;
+import jalview.structures.models.AAStructureBindingModel.ColourBy;
 import jalview.util.BrowserLauncher;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -113,14 +114,14 @@ public class AppJmol extends StructureViewerBase
     initMenus();
     if (leaveColouringToJmol || !usetoColour)
     {
-      jmb.setColourBySequence(false);
+      jmb.setColourBy(ColourBy.Viewer);
       seqColour.setSelected(false);
       viewerColour.setSelected(true);
     }
     else if (usetoColour)
     {
       useAlignmentPanelForColourbyseq(ap);
-      jmb.setColourBySequence(true);
+      jmb.setColourBy(ColourBy.Sequence);
       seqColour.setSelected(true);
       viewerColour.setSelected(false);
     }
@@ -193,7 +194,7 @@ public class AppJmol extends StructureViewerBase
     alignAddedStructures = alignAdded;
     useAlignmentPanelForSuperposition(ap);
 
-    jmb.setColourBySequence(true);
+    jmb.setColourBy(ColourBy.Sequence);
     setSize(400, 400); // probably should be a configurable/dynamic default here
     initMenus();
     addingStructures = false;