[Chimera-users] hbonds and addh geometry

Jim Procter jimp at compbio.dundee.ac.uk
Mon Jan 22 04:16:34 PST 2007

Hi all.

Has anyone noticed and/or fixed the slight problem with applying the 
hbonds command (without 'sloppy' bond geometry allowed) after adding 
hydrogens to a structure with addh ?
The identified hbonds are marked between donor and acceptor, but the 
donor's proton seems often seems to lie some way off the hbond vector by 
a seemingly consistent amount, suggesting a systematic error in the addh 
protonation geometry.

As an aside to this, it would be very nice to be able to re-connect the 
detected hydrogen bonds so that the bond vector lies between the proton 
and the acceptor, rather than between the heavy atoms. Does anyone have 
a script to do this ?

thanks in advance!
Jim Procter

J. B. Procter (VAMSAS Project) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk 

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