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File Formats

Mapping

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

Contacts

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

Troubleshooting

I'm having trouble with the Java viewer displaying my job, what is wrong?

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.

My question isn't answered here, how can I reach you?

Please use the contact form on our lab website

Structural Bioinformatics Lab
Boston University