Mapping results are provided in a PDB file where the crossclusters are put into separate chains from the protein. Additionally, they are separated by a HEADER record, which allows some viewers (e.g. PyMol) to separate them into separate objects
The server uses HBPlus to count the contacts between probes and the protein. This uses all the probes before clustering. The format of these files is:
Residue_Number Chain Residue_Name Num_Contacts
As an example, this shows 18 contacts with ILE10 on chain A of the protein
10 A ILE 18
It is more than likely that you need to increase the amount of memory available to the java applet. The PDB has a good description on increasing the memory available to Java.
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