[Chimera-users] Making Hydrogen Bonds

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 9 09:55:45 PST 2008

Hi Ahir,
I'd just like to add:

(A) both ways Eric described could also be done with the "findhbond"  
command - see the keywords selRestrict, intramodel, intermodel.  You  
could use the "select" command to create the selections beforehand.

(B) if you just want to draw lines between specific known pairs of  
atoms, you can use the "PseudoBond Reader" tool instead of FindHBond.   
This reads a text file you previously created listing the pairs of  
atoms and the colors of the lines to be created.

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 8, 2008, at 7:09 PM, Eric Pettersen wrote:

> 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

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