Protein Engineering, 16, 713-715 (2003)
	DOI:10.1093/protein/gzg100

Since the C=O directions essentially alternate by 180^o in sheets, FP⁰ will be dominated by alternating white and black bars in such regions. On the other hand, the C=O directions are essentially parallel in helices, resulting in black equilateral right angle triangles located above the diagonal.

The secondary fingerprint matrices FP¹ and FP² are defined to allow the differentiation between parallel and antipararllel sheets, and between different packing of helices, respectively. FP¹ is defined by the angle between the line connecting the carbonyl carbons of residue i and j and the line connecting the C and N atoms of residue i:

while FP² is defined by the angle between the line connecting the carbonyl carbons of residue i and j and the normal to the plane formed by the C and O atoms of residue i and the N of residue i+1:

The information in FP¹ encodes the direction the backbone path takes. Generally, FP⁰ contains the most information and in several cases it can serve in itself to characterize the fold. Combining two maps results in a matrix whose elements can take four values.

The examples below show that the minima (as a function of the alignment of a motif with a protein containig that motif) in the fingerprint fit tracks the minima in the RMSD. Note that 50% difference in fingerprint maps corresponds to random aligment.

In the eaxmple below, the two four-helix bundle proteins difer only in the orientation of a single helix. The resulting fingerprints have obviously different pattern.