On Jan 3, 2006, at 9:59 a, Timothy Driscoll wrote: > On Jan 3, 2006, at 8:53 a, Herbert J. Bernstein wrote: > >> The logic used by RasMol for H-bonds is as follows. I would be happy >> to add alternate approaches, but this one will remain the default >> so as not to mess up existing scripts: >> >> Quoting from the Sayle-Martz RasMol FAQ >> >> "For protein, regions of alpha helix or beta-sheet are identified by >> application of the algorithm of Kabsch and Sander. Hydrogen bonds are >> assigned when a distance-dependent electrostatic energy of >> interaction between donors and acceptors falls below a threshold >> value. No reference is made to phi or psi angles. >> > > why doesn't RasMol use dihedral angles in hbond calculations? > sorry; I meant secondary structure assignment, not hydrogen bonding. just curious. are hydrogen bond patterns better in some way? tim -- Timothy Driscoll em: molvisions at mac.com molvisions - see. grasp. learn. ph: 919-368-2667 <http://www.molvisions.com/> im: molvisions usa:virginia:blacksburg tx: molvisions at vtext.com