[Chimera-users] Formation of coordination bond

Eric Pettersen pett at cgl.ucsf.edu
Mon May 18 10:14:06 PDT 2009

Hi Enrico,
	As Elaine pointed out, you can't form a covalent bond between two  
models (since that's the definition of "model" in Chimera).  Forming a  
pseudobond as Elaine outlines is one possibility.  The other  
alternative is to combine the two models into one by using the  
"combine" command or the "copy/combine" button of the Model Panel.   
Once you have a single model you can then use the "bond" command to  
form a bond between the atoms.
	However, I recommend Elaine's approach unless there's a specific  
reason you need a single model (such as writing out a PDB file without  
MODEL records).


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On May 18, 2009, at 9:38 AM, Elaine Meng wrote:

> 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
> atoms.
> 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:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html
> 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)
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules
> 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
> -----
> Elaine C. Meng, Ph.D.
> 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 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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> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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