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

Kevin Karplus karplus at soe.ucsc.edu
Tue Jan 3 10:11:03 EST 2006

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.

Currently, most crystallographers seem to use the DSSP definitions of
secondary structure---not because they are "right" but because they
are acceptable and do not need to be defended.  I doubt that anyone
would quibble if the STRIDE definitions were used instead---the main
effect would be changes of +-1 residue on the ends of helices.

Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
(Senior member, IEEE)	(Board of Directors, ISCB)
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
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