JAL-3390 showSelectedChains pulled up to base class for Jmol/Chimera

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 2a9a698..d820273 100644 (file)
--- 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());
   }