I was going through the tutorial and was displaying a jmol panel. When I selected Show SCOP Domains for the color on the selection, I received a FileNotFoundException. A review of the Berkeley site shows that they changed from http to https for the scheme. They also appear to have changed the path portion of the URL in version 2 from 'scop' to 'scope.'

All of the unit tests worked before and after this change. I tried to create a unit test to show the failure, fix it, and run the unit test to show that it was fixed, but I couldn't quite follow the path to get to the ScopInstallation code from the Swing application.

To recreate my original error, the following code can be used (derived from the tutorial).

         Structure structure = StructureIO.getStructure("4FRW");
         System.out.println(StructureTools.getNrAtoms(structure));
         StructureAlignmentJmol jmolPanel = new StructureAlignmentJmol();

         jmolPanel.setStructure(structure);

         // send some commands to Jmol
         jmolPanel.evalString("select * ; color chain;");
         jmolPanel.evalString("select *; spacefill off; wireframe off; cartoon on;  ");
         jmolPanel.evalString("select ligands; cartoon off; wireframe 0.3; spacefill 0.5; color cpk;");