On Tue, 3 Jan 2006, Kevin Karplus wrote: > Although RASMOL *claims* to use the DSSP algorithm for identifying > Hbonds, it does not seem to use the entire algorithm as it reports > many erroneous H-bonds that DSSP omits on geometric grounds. > Rasmol seems to use only the distance and not the geometry of the hbond. I'm pretty certain that RasMol's implementation is an accurate implementation of the original DSSP algorithm. In the Kabsch and Sander definition, the existence of a structural hydrogen bond is not based directly on either distance or geometry, but as a threshold on the coulombic interaction energy. It is the relative interaction energies of H..O, N..O, H..C and N..C that defines the acceptable geometries. The interested reader can refer to the distance vs. angle graphs provided in Fig. 1 of "Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features", Wolfgang Kabsch and Christian Sander, Biopolymers, Vol. 22, pp. 2577-2637, 1983. Admittedly, the Stride definition of a backbone hydrogen bond given in "Knowledge-based Protein Secondary Structure Assignment", Dmitrij Frishman and Patrick Argos, Proteins: Structure, Function, Genetics, Vol. 25, pp. 566-579, 1995 is more advanced, but at the time RasMol was written DSSP definitions were clearly the de facto standard. If anyone knows of a discrepancy between between RasMol's secondary structure assignment and those assigned by DSSP, let me know and I'll investigate. Be warned that in the Kabsch and Sander definition there may be numerous backbone hydrogen bonds that are then not recognized as forming part of a standard secondary structure unit. For protein sidechain and protein-ligand hydrogen bonding, one might consider a more general definition such as the one used in GRID: D.Boobbyer, P.Goodford, P.McWhinnie and R.Wade, "New Hydrogen-Bond Potentials for Use in Determining Energetically Favorable Binding Sites on Molecules of Known Structure", Journal of Medicinal Chemistry, Vol.32, No.5, pp.1083-1094, 1989. Roger -- Roger Sayle, E-mail: roger at eyesopen.com OpenEye Scientific Software, WWW: http://www.eyesopen.com/ Suite 1107, 3600 Cerrillos Road, Tel: (+1) 505-473-7385 Santa Fe, New Mexico, 87507. Fax: (+1) 505-473-0833