The correspondence used to compute CARMSD for a pair of proteins is 1 to 1.
If two proteins A and B are to be optimally superposed, both PDB files
(A.pdb and B.pdb) must have the same numbers of alpha carbons.
The first alpha carbon in A.pdb will be matched to the first alpha carbon in
B.pdb, and so on.

Clustering up to 20,000 PDB files should work on most machines.
Workstations with a lot of memory will be able to cluster even more files.

Examples:
---------

* to perform exact clustering using a fixed cutoff value of 3.0 Angstroms:

durandal -i [file_containing_one_PDB_filename_per_line] -d 3.0 -o out -s -v

* there is also another tool included, to compute CARMSD of many files
  versus a reference one (the first in the list is considered the
  reference):

ranker [file_containing_one_PDB_filename_per_line]

If you want to know more about how the software is working, you can have a look
at http://bioinformatics.oxfordjournals.org/content/27/7/939

Don't hesitate to ask if you encounter any problem while using the software.

Best regards,
Francois Berenger.