The program reads a file containing a list of PDB files to analyze. For each protein domain (chain) in the PDB file the program removes one by one the outermost heavy atom. The atom with the larges circular variance (CV) is considered to be the outermost.

Whenever the atom removed is part of the backbone, and the nearest (or end) break residue is more then a user-specified number of residues (break residue distance) away the residue it is part of is marked as a special one - tentatively suggested to be an Achilles' heel. The program lists all of these residues during the run.

At the end of the run phe program prints (broken down by secondary structure element and overall)

• The average percent of backbone breaks marked
• The average percentage of each amino acind in the whole set
• The average percent of each amino acind among the marked backbone break residues
• The ratio of the break residue percentage to the average amino acid percentage
• The average percentage of each amino acind in the whole set on the surface
• The ratio of the break residue percentage to the average amino acid surface percentage
• The average side-chain length of the break residues
• The average side-chain length of the non-break residues
• The molecular volumes of the amino acids
• The hydrophobicities of the amino acids

Also correlations between the two kind of preak point propensities and side chain length, amino acid volume and hydrophobicity are also calculated.

The program can be run as
cvshave [directive argument] [directive argument]...
where

Directive	Argument	Default
-lf	File listing the PDB files to process
-cv	CV cutoff	15.0
-rd	Break residue distance	10
-iv	Output level	1
-ns	Number of files to skip	0
-ns	Number of files to process	all
-of	Output file	cvshave.out

If only the program name is typed, the user will be promptes for the input information.

The program is written in Fortran-77 and can be compiled with any Fortran compiler, including GNU fortran:

f77 -o cvshave cvshave.f

to obtain the executable cvshave