X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=5f1a70bcc1dbe1e5582e96ab974d015cda624b38;hb=83f6c6309e9705037a0853a26da74821c9d4fd12;hp=4a091b20f30b19e3ab34601f23250975daf88d36;hpb=31b00a6d85b8a1b4032f11f448911938004a5f6b;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 4a091b2..5f1a70b 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -33,6 +33,7 @@ import jalview.structure.*;
 import jalview.datamodel.PDBEntry;
 import jalview.io.*;
 import jalview.schemes.*;
+import jalview.ws.EBIFetchClient;
 
 import org.jmol.api.*;
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
@@ -413,6 +414,7 @@ public synchronized void addSequence(SequenceI [] seq)
 
   public void seqColour_actionPerformed(ActionEvent actionEvent)
   {
+    lastCommand = null;
     colourBySequence = seqColour.isSelected();
     colourBySequence(ap.alignFrame.alignPanel);
   }
@@ -588,17 +590,13 @@ public synchronized void addSequence(SequenceI [] seq)
       resetLastRes.append(":" + chain);
     }
 
-    eval.append(";color gold;wireframe 100");
+    eval.append(";wireframe 100;"+eval.toString()+".CA;");
 
-    Color col = new Color(viewer.getAtomArgb(atomIndex));
+    resetLastRes.append(";wireframe 0;"+resetLastRes.toString()+".CA;spacefill 0;");
 
-    resetLastRes.append(";color["
-                        + col.getRed() + ","
-                        + col.getGreen() + ","
-                        + col.getBlue() + "];wireframe 0");
+    eval.append("spacefill 200;select none");
 
     viewer.evalStringQuiet(eval.toString());
-
   }
 
   public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
@@ -655,11 +653,7 @@ public synchronized void addSequence(SequenceI [] seq)
     {
       for (int m = 0; m < mapping.length; m++)
       {
-        System.out.println(mapping[m].getSequence().getName()+" "+sequence[s].getName()+" "
-        +((mapping[m].getSequence() == sequence[s])
-          +" "+(ap.av.alignment.findIndex(sequence[s]))));
-
-                           if (mapping[m].getSequence() == sequence[s]
+        if (mapping[m].getSequence() == sequence[s]
             && ap.av.alignment.findIndex(sequence[s])>-1)
         {
           for (int r = 0; r < sequence[s].getLength(); r++)
@@ -851,7 +845,8 @@ public synchronized void addSequence(SequenceI [] seq)
     if (chainId != null)
       picked+=(":"+chainId.substring(1, chainId.length()));
 
-    picked+=".C";
+    picked+=".CA";
+
 
     if (!atomsPicked.contains(picked))
     {