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 Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu