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

Timothy Driscoll molvisions at mac.com
Tue Jan 3 10:57:19 EST 2006

On Jan 3, 2006, at 10:11 a, Kevin Karplus wrote:
> The debate over whether to include torsion angles in determining
> secondary structure is an old one (DSSP vs. STRIDE).  It turns out
> that on high-quality x-ray structures it doesn't make much difference
> what algorithm you use---the disagreements come down to matters of
> opinion about where the edges of secondary structures are.  The
> biggest differences are on NMR structures, where insufficient data or
> insufficient refinement often results in failure to get Hbonds within
> the recognition range of algorithms like DSSP.  Then using the phi and
> psi angles can help compensate for the noisy positions of the donor
> and acceptor atoms.

hi Kevin,

thanks for the clarification.  how would you define a 'high-quality'  
x-ray structure?  is there a generally accepted threshold for  
resolution or RMSD?


Timothy Driscoll                                em: molvisions at mac.com
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