[Chimera-users] Formation of coordination bond

Elaine Meng meng at cgl.ucsf.edu
Mon May 18 09:38:07 PDT 2009

Dear Enrico,
Chimera doesn't allow adding a bond between two different models  
(structures opened from two different files), but if you mainly want  
the appearance of a bond, you can create a "pseudobond" connecting the  

Pseudobonds are just lines drawn between any pair of atoms.  You can  
control their style, thickness, color, and labels.  To make  
pseudobonds, create a text file where each line gives the two atoms to  
be connected, and the desired color and optional label.  In your case  
the file might be only one line.  Then use the Pseudobond Reader tool  
to open the text file and create the pseudobond(s).  Here is the  
description of that tool and the file format:

For further changes such as line style and color, open Pseudobond  
Panel (under Tools... General Controls), and in that dialog choose  
your pseudobonds on the left side and click the "attributes..." button  
on the right.  That will bring up another window with options to  
adjust the display.  Such changes could also be done with the  
"setattr" command, but it is trickier.  You may want to make your new  
pseudobond look the same as other metal complex pseudobonds (default  
medium purple, linewidth 2.5, dashed)

Currently there is no command to add pseudobonds.  You could make the  
pseudobond ahead of time and undisplay it, then show it later within a  
script, using the "setattr" command:

setattr p display false ions z<4
setattr p display true ions z<4

where the "ions z<4" part limits the effect to only pseudobonds around  
ions.  I hope this helps,
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 May 18, 2009, at 8:22 AM, Enrico Morelli wrote:

> Dear all,
> We would like to know if is it possible, when we have two molecules
> docked together, to form a coordination bond between a metal ion
> present in one of the two molecules and a donor atom of the
> other molecule, in such way forming a covalent bond between the two
> proteins.
> Thanks

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