[Chimera-users] hbonds and addh geometry

Eric Pettersen pett at cgl.ucsf.edu
Mon Jan 22 11:42:12 PST 2007

On Jan 22, 2007, at 4:16 AM, Jim Procter wrote:

> 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.

Hi Jim,
	Added hydrogens are positioned to point toward the estimated  
position of the acceptor's nearest lone pair, which can put them  
somewhat "off line" with respect to the nucleus-nucleus depiction of  
the hydrogen bond.

> 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 ?

	I've attached a Python script which shifts the donor end of H-bonds  
from the heavy atom to the hydrogen nearest the acceptor.  You can  
run it by opening the file with File->Open... or the "open" command.   
You are right that it would be nice to be able to do this directly in  
Chimera.  Our thinking is to add it to FindHBond as an option that  
defaults to "on" -- or maybe not even an option, just always do it.   
If anyone has opinions, feel free to chime in.  We'll try to get  
something into the next release or two.


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

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