[Molvis-list] exporting _good_ h-bonds (was: export Chime h-bonds)

Timothy Driscoll molvisions at mac.com
Tue Jan 3 10:00:45 EST 2006

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?

Timothy Driscoll                                em: molvisions at mac.com
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