do dssp

The do_dssp program is actually just an interface to the DSSP program, used to calculate the secondary structure evolution of a protein over time.  You must have DSSP installed on your system before do_dssp will work.  The do_dssp further assumes that the dssp executable is located in /usr/local/bin.  If this is not the case, you must set the DSSP environment variable accordingly.  For bash:

export DSSP=/path/to/dssp

For csh/tcsh:

setenv DSSP /path/to/dssp

To properly use do_dssp, the group chosen for analysis should be "MainChain," or a custom group derived from it.  A common mistake is to select "Protein," which causes the program to hang.  Since DSSP is only measuring backbone torsion angles, the rest of the protein atoms (i.e., side chains) are unimportant in secondary structure calculation, thus causing a hang.  The output is an .xpm file, which can be converted to an .eps file with xpm2ps.