[Molvis-list] export Chime h-bonds

Kevin Karplus karplus at soe.ucsc.edu
Mon Jan 2 17:04:52 EST 2006

Raymond Keller asked about programs that report sidechain H-bonds, in
particular wondering what access there was to Chime's method for
finding them.  I can't be of much help on this one.

I'm not familiar with the programs available, because I wrote my own
for the undertaker program.  It turns out to be fairly tricky to get
"real" hbonds, and there is always an arbitrary cutoff for whatever
properties are measured (distances, angles, ...).  There are also
questions about whether weak Hbonds (such as donor hydrogens on
araomatic carbons, or acceptors in the center of an aromatic ring)
should be counted.

I would be a bit uncomfortable using someone else's code, unless I
spent many hours reading it carefully and seeing how all the arbitrary
decisions had been made.

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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