X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=d82027313276531c367a03a03dabb5e138b0dc30;hb=a663c1c844de90b4c125dbbcf5c8b953b00a809d;hp=2a9a69890203d67731d5ccd3a1cbe1d00ef117e4;hpb=5c6564f903f75960af960720a8635ab8709afc37;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 2a9a698..d820273 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -133,9 +133,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   /**
-   * prepare the view for a given set of models/chains. chainList contains
-   * strings of the form 'pdbfilename:Chaincode'
+   * prepare the view for a given set of models/chains. chainList contains strings
+   * of the form 'pdbfilename:Chaincode'
+   * 
+   * @deprecated now only used by applet code
    */
+  @Deprecated
   public void centerViewer()
   {
     StringBuilder cmd = new StringBuilder(128);
@@ -1440,10 +1443,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     {
       cmd.append("hide *;");
 
-    AtomSpecModel model = getShownResidues(av);
-    String atomSpec = JmolCommands.getAtomSpec(model);
+      AtomSpecModel model = getShownResidues(av);
+      String atomSpec = JmolCommands.getAtomSpec(model);
 
-    cmd.append("display ").append(atomSpec);
+      cmd.append("display ").append(atomSpec);
     }
     else
     {
@@ -1452,7 +1455,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     cmd.append("; cartoon");
     if (refocus)
     {
-      cmd.append("; zoom 100");
+      cmd.append("; zoom 0");
     }
     evalStateCommand(cmd.toString());
   }