[Chimera-users] How to make bonds between two pdb files

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 6 13:06:50 PST 2008

Hi Ann,
Chimera won't move the atoms when it creates the bond, it simply adds  
the bond.  So one issue is that the user needs to manually position  
one structure relative to the other before adding the bond.

To move the structures separately with the mouse, you can toggle their  
activation status, for example using the Active checkboxes in the  
Model Panel (under Tools... Favorites).

The second issue is that you can't bond atoms in different models, so  
after the desired relative position has been attained, combine them  
using the new "combine" command
or "copy/combine" function in the Model Panel (you need a recent daily  
build for these to be available).

Then the bond can be added with the command "bond"

or Build Structure (under Tools... Structure Editing), Add/Delete  
Bonds section:

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 Nov 5, 2008, at 3:40 PM, Ann Spevacek wrote:
> Hello -
> I am trying to make a bond between a protein and a polysaccharide
> chain in Chimera and am not quite sure how to do it.  I am also
> curious as to whether the program will take into account interactions
> such as sterics when it generates the bond.
> Any guidance will be greatly appreciated!
> Thanks,
> Ann Spevacek
> Millhauser Lab

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