Click here or contact me to download PARS software. 

PARS is designed for calculating the number of sequence fragments (mono, di and three-peptides), with assigning their conformation in secondary structure terms. As input, you need the structural file format, *.DSSP, for your structure. This file format is a plain text file format with DSSP extension, containing necessary secondary structure data for any residues.  

Working with PDB structural file format - obtained from Protein Data Bank, you have to convert it to DSSP format. This can be done in some ways. See these pages for more information:

http://www.cmbi.ru.nl/dssp.html

or

http://www.cmbi.ru.nl/xssp/

A DSSP file format sample is here.

After preparing your input, you can use PARS software. Here is graphical step by step help:

(Crystal Structure of Bovine Serum Albumin, PDB ID: 4f5s explained here)  

1

-Load your input:

Calculate fragment frequencies and save the results:

A sample of graphical output:

Also, the outputs are savable as two format, both in PARS extensions. (Format1, Format2)

For any question, specially reporting bugs, contact: heshmati@znu.ac.ir or bioinf.comp.biol@gmail.com