List of pairs allows one to upload a text file specifying the pairs of structures from the file set that should be matched against each other. The file may be gzipped or compressed. It must contain two columns, the left one specifying query structures, and the right one - corresponding to them search targets. Name of structures must match file names in the file set.  
Example: 

1abc.pdb  2abc.pdb
1abc.pdb  3abc.pdb
2abc.pdb  3abc.pdb
Upon receiving such list of pairs, SSM will look for structures 1abc.pdb, 2abc.pdb and 3abc.pdb in the uploaded file set and then perform 3 matches: 1abc.pdb against 2abc.pdb and 3abc.pdb, and 2abc.pdb against 3abc.pdb.

NOTE 1: you need to specify the file names in the pairlist rather than structure names. E.g. if files are gzipped or compressed before making the file set tarball, do not forget to specify ".gz" (".Z" if compressed) extensions for each file.  
NOTE 2: if your file set tarball has subdirectories, they must be explicitely given for each file name in the list of pairs. The above example assumes no directory structure in the tarball.  
NOTE 3: pairs of structures with file names not found in the file set tarball are silently ignored.  
NOTE 4: never change the ".gz" and ".Z" file extensions of the pair list if you gzip or compress it before uploading.