File set allows one to upload a set of structures to be taken as search targets. The structures must be represented by valid PDB or mmCIF coordinate files (or any combination of them) and be packed into a tarball. The corresponding UNIX command is 

tar cvf tarball.tar *.pdb
where "*.pdb" exemplifies the PDB files that should be included into the tarball. In order to make the upload faster, the files may be be gzipped or compressed, for example: 
gzip *.pdb
tar cvf tarball.tar *.pdb.gz
or 
compress *.pdb
tar cvf tarball.tar *.pdb.Z
You may as well gzip/compress the entire tarball: 
tar cvf tarball.tar *.pdb
gzip tarball.tar
or 
tar cvf tarball.tar *.pdb
compress tarball.tar
and the resulting "tarball.tar.gz" ("tarball.tar.Z") is just as good for upload. However, we advise you to gzip/compress the structures, rather than the tarball, because it saves disk space on our server.

NOTE 1: the tarball should contain only coordinate files. In most cases, non-coordinate files (or invalid PDB/mmCIF files) will be safely and silently ignored, however there is a chance that they confuse the server.  
NOTE 2: never change the ".tar" and ".gz", ".Z" file extensions of the tarball and of the structures, if the latter were gzipped/compressed.  
NOTE 3: it is perfectly Ok to make a tarball with directory structure (for example, to tar a whole directory). However, keep in mind that you may have difficulties in differentiating between same-named structures from different sub-directories in the SSM output.