[Chimera-users] hydrogen bond representation

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 4 08:56:34 PDT 2009

Hi Bala,
As mentioned in the FindHBond page,

"All potential H-bonding interactions fulfilling the criteria are  
shown." In other words, each is possible taken individually based on  
distances and angles, but it will not necessarily be possible to form  
all of them at the same time.  If the structure does not include  
hydrogens, for example, the H-bonds possible from a hydroxyl oxygen  
might require the OH hydrogen to be in different places.

The H-bonds are shown with pseudobonds, and there are several ways to  
change their appearance.  The line style is actually an attribute of  
the pseudobond group.  Ways to change this:

(a) Ctrl-click to select one H-bond, press up arrow to expand  
selection to all H-bonds, open Selection Inspector, inspect  
"Pseudobond group" and change the "line style"

(b) start Pseudobond Panel (under Tools... General Controls), click  
on group name "hydrogen bonds" on the left and then "attributes" on  
the right, change "line style"

(c) use command "setattr" e.g. something like:
setattr g lineType 3

The attribute name (e.g. lineType) and what values mean what (e.g. 3  
= dotted, which just looks like shorter dashes to me) are shown in  
the balloon help when you put the mouse over the attribute dialogs  
mentioned in (a) and (b).

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 4, 2009, at 8:33 AM, Bala subramanian wrote:

> Friends,
> Is there any way to represent hydrogen bonds as dotted lines  
> instead of a solid line in Chimera. Sometimes hbond analysis in  
> chimera shows same atom to be involved in two hydrogen bonds, why  
> is it so ?
> Thanks,
> Bala

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