Running from the command line, user simply enters a list of file names and the script retrieves each pdb file from RCSB and reports the number and the percetage of each of the 20 common amino acid types present in each protein.

An alternative is provided in the script for working with a series of PDB or MSV files in user's local working directory. User can also use this option to run from within the Discovery Studio client, but only one protein PDB or MSV file can be specified as inputFile. See comments in the script file.