X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=caaffa2869afb277da11d5e06fbf0bf55ee6caf0;hb=11cce1c1e065d4430400ad414460ae643b51fbfe;hp=7939d9bf4b3fa60c47ed864fc4fd54ec22363e66;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 7939d9b..caaffa2 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.appletgui;
 
@@ -117,20 +116,17 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
     this.protocol = protocol;
     if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
     {
-      if (jalview.bin.JalviewLite.debug)
+      if (protocol.equals(AppletFormatAdapter.PASTE))
       {
-        System.err.println("Setting PDB id for file " + pdbentry.getFile());
-        if (protocol.equals(AppletFormatAdapter.PASTE))
-        {
-          pdbentry.setId("PASTED PDB"
-                  + (chains == null ? "_" : chains.toString()));
-        }
-        else
-        {
-          pdbentry.setId(pdbentry.getFile());
-        }
+        pdbentry.setId("PASTED PDB"
+                + (chains == null ? "_" : chains.toString()));
+      }
+      else
+      {
+        pdbentry.setId(pdbentry.getFile());
       }
     }
+
     if (jalview.bin.JalviewLite.debug)
     {
       System.err
@@ -544,16 +540,18 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
     resetLastRes.setLength(0);
     resetLastRes.append("select " + pdbResNum);
 
+    eval.append(":");
+    resetLastRes.append(":");
     if (!chain.equals(" "))
     {
-      eval.append(":" + chain);
-      resetLastRes.append(":" + chain);
+      eval.append(chain);
+      resetLastRes.append(chain);
     }
 
-    eval.append(";wireframe 100;" + eval.toString() + ".CA;");
+    eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
 
     resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
-            + ".CA;spacefill 0;");
+            + " and not hetero; spacefill 0;");
 
     eval.append("spacefill 200;select none");