From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 21 Nov 2014 14:33:08 +0000 (+0000)
Subject: JAL-1528 found and readded Colour by Chain ('rainbow color')
X-Git-Tag: Release_2_8_2b1^2~18
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5720f2cea034f014f366886b3cb9a170a909e988;p=jalview.git

JAL-1528 found and readded Colour by Chain ('rainbow color')
---

diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
index e866597..236701a 100644
--- a/help/html/features/chimera.html
+++ b/help/html/features/chimera.html
@@ -133,6 +133,8 @@ atoms in the displayed structures. For comprehensive details of Chimera's comman
 		they are insertions (relative to the associated sequence in the
 		alignment) and grey if they are N or C terminal flanks outside the
 		region mapped to the alignment window's sequence.</em></li>
+		<li><strong>By Chain<br>
+		</strong><em>Uses the Chimera 'rainbow chain' command to apply a different colour to each chain.</em></li>
 		<li><strong>Charge &amp; Cysteine<br>
 		</strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
 		Glutamic Acid) residues in red, and cationic (Lysine or Arginine)
diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 5d3667b..cabee76 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -107,7 +107,7 @@ action.change_params = Change Parameters
 action.apply = Apply
 action.apply_threshold_all_groups = Apply threshold to all groups
 action.apply_all_groups = Apply to all Groups
-action.by_chain = By chain
+action.by_chain = By Chain
 action.by_sequence = By Sequence
 action.paste_annotations = Paste Annotations
 action.format = Format
diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 090b61d..fb03f04 100644
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -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()
diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index cfac4ef..02865e1 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -144,9 +144,6 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable,
       _alignwith = new Vector<AlignmentPanel>();
     }
 
-    // no colour by chain command in Chimera?
-    chainColour.setVisible(false);
-
     // save As not yet implemented
     savemenu.setVisible(false);