[Chimera-users] how to make a bond

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 15 09:47:21 PST 2007

Hi Dominique,
I guess you mean you just want to show a solid line or a stick?

The dotted line is a "pseudobond" and this recent chimera-users  
message describes how you could change its appearance or hide it:

Two approaches were mentioned in that message.
(a) the Selection Inspector approach allows an individual selected  
pseudobond to be hidden or changed to stick

(b) the Pseudobond Panel approach allows the attributes of the whole  
group (usually all the pseudobonds to one metal ion) to be changed at  
once.  attributes include whether the line is dashed or not, the line  
color, etc.

If you really care that it is considered a bond and not a pseudobond,  
you could hide the pseudobond (or close its group in the Pseudobond  
Panel), select the 2 atoms, and then use the command

bond sel

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 14, 2007, at 2:15 AM, dominique matt wrote:

> I want to draw a bond between two atoms which appear linked by a  
> dotted line. This is often the case when one atom is a metal.
> How can I draw the bond ?
> Thank you for your help
> Kind regards
> Dominique MATT
> Strasbourg

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