Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more' into...

diff --combined src/jalview/gui/StructureViewerBase.java
index 8ac23ef,8290dd9..349871d
--- 1/src/jalview/gui/StructureViewerBase.java
--- 2/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@@ -47,6 -47,7 +47,7 @@@ import javax.swing.event.MenuListener
  
  import jalview.api.AlignmentViewPanel;
  import jalview.bin.Cache;
+ import jalview.bin.Console;
  import jalview.datamodel.AlignmentI;
  import jalview.datamodel.PDBEntry;
  import jalview.datamodel.SequenceI;
@@@ -814,7 -815,7 +815,7 @@@ public abstract class StructureViewerBa
        {
          sp.append("'" + alignPanel.getViewName() + "' ");
        }
-       Cache.log.info("Couldn't align structures with the " + sp.toString()
+       Console.info("Couldn't align structures with the " + sp.toString()
                + "associated alignment panels.", e);
      }
      return reply;
@@@ -1160,7 -1161,7 +1161,7 @@@
        } else {
            if (processingEntry.hasRetrievalUrl())
            {
 -            String safePDBId = java.net.URLEncoder.encode(pdbid,"UTF-8");
 +            String safePDBId = java.net.URLEncoder.encode(pdbid,"UTF-8").replace("%","__");
                       
              // retrieve from URL to new local tmpfile
              File tmpFile = File.createTempFile(safePDBId,