X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=9b9c239fd8808fb362ad1b2d325308d223c6c7b5;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=090b61d926901eecca203eb3b5c576e0490b3577;hpb=cedd8bb81245ba719e6d54688d763e341b3cc695;p=jalview.git

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 090b61d..9b9c239 100644
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -343,8 +343,7 @@ public abstract class JalviewChimeraBinding extends
   public void colourByChain()
   {
     colourBySequence = false;
-    // this is not a valid Chimera command; is there one? Menu option hidden
-    evalStateCommand("select *;color chain",false);
+    evalStateCommand("rainbow chain", false);
   }
 
   public void colourByCharge()
@@ -783,7 +782,7 @@ public abstract class JalviewChimeraBinding extends
 
   private void waitForChimera()
   {
-    while (viewer.isBusy())
+    while (viewer != null && viewer.isBusy())
     {
       try {
         Thread.sleep(15);
@@ -955,7 +954,7 @@ public abstract class JalviewChimeraBinding extends
     }
   }
 
-  boolean debug = true;
+  boolean debug = false;
 
   private void log(String message)
   {
@@ -964,8 +963,8 @@ public abstract class JalviewChimeraBinding extends
 
   private void viewerCommandHistory(boolean enable)
   {
-    log("(Not yet implemented) History "
-            + ((debug || enable) ? "on" : "off"));
+    // log("(Not yet implemented) History "
+    // + ((debug || enable) ? "on" : "off"));
   }
 
   public void loadInline(String string)