Beta-test of new functionality in the MDB

• A simple search interface, allowing the display of sites found using our MSIT program, which automatically recognizes the first and second liganding shells in metal sites, and deals with cluster and multinuclear sites
• The new MDB viewer showing a couple of example structures.
• An example of integrating QM/DFT information, generated in our Program Project, with the other components of the MDB.
• A prototype of the Metal-binding Site Evaluator (MSE), which allows the researcher to upload his/her valid PDB file and will apply our tools to generate a full report of existing the metal-binding sites, geometries, etc. in the macromolecular structure. This is an indexing tool, not a predictive one.
• Chime output - only if you have a Windows or Mac machine with the appropriate plugin from MDL. The aim there is to show the structures we can extract now with the new metal-binding site indexing java application (which is in late beta)
• XML examples - not documented at all. Just to show the CML/XML output from the java application mentioned above, and how we can parse it and recreate an object from the file. The object example is very simplistic but demonstrates the hierarchy of objects parsed.
  • Parsing of CML file
  • Same as above, but compact
  • Colorization of CML file
  • File used above (MSIE 5.x will display it)
  • Metal binding object showing the contained shells, residues and atoms as concentric boxes using tables.