[Chimera-users] Making Hydrogen Bonds

Eric Pettersen pett at cgl.ucsf.edu
Mon Dec 8 19:09:50 PST 2008

On Dec 5, 2008, at 4:11 AM, Ahir Utsav Pushpanath wrote:

> Hello. I was wondering whether you could tell me whether there is a  
> graphic/command line option enabling me to create "hydrogen bonds"  
> between my specific residue+ligand only. Or, whether it is possibly  
> to manually draw hydrogen bonds between atoms. In addition, using  
> the FindHbonds tool, is it possible to find H bonds between only  
> ligand + a specific type of residues, for example hydrophobic or  
> valine etc.

Hi Ahir,
	What I would do if I were you would be to select the residues you  
care about along with the ligand, then in the FindHBonds tool check  
the "Only find H-bonds with" box and change the menu to "both ends  
selected".  This will find only H-bonds completely contained in your  
selection.  This may find a few H-bonds you don't want:  ones between  
the non-ligand selected residues, and ones within the ligand itself.   
You can select the ones you don't want, and bring up the Selection  
Inspector (by clicking on the green button at the lower right of the  
main Chimera window) and change "displayed:" to "off".  [control- 
double clicking on an H-bond will also bring up the Selection  
Inspector for it]
	Another alternative is to open a second copy of your structure.   
Select the residues you want in one model and the ligand in the  
other.  Then do the "both ends selected" thing like in the above  
paragraph, but also change "Find these bonds:" (upper right of the  
FindHBonds dialog) to "inter-model".  Then you will only get H-bonds  
between your selected residues and the ligand and no extra H-bonds.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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