[Chimera-users] Making Hydrogen Bonds

[Elaine Meng]

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.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/select.html>

(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.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html 
 >

Best,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html



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