[Chimera-users] Making Hydrogen Bonds
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.
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.
UCSF Computer Graphics Lab
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