The protein chains are arranged in order of the quality of atomic coordinate data.
Earliest chain is taken for a representative and compared with every other chain.
Similar chains to the representative on amino acid sequence or structure similarity are classified into the same group with the representative. Elimination and sort options make various data sets to be classified into groups afterward. Yes' option causes elimination of chains by the following threshold . Set 'threshold' . Independently of elimination, chains are sorted by keys of factors .