[Chimera-users] Protein Design

Eric Pettersen pett at cgl.ucsf.edu
Mon Jun 13 10:36:52 PDT 2011

On Jun 11, 2011, at 1:34 PM, Jared Adolf-Bryfogle wrote:

> Hi All,
> I am trying to work on the design of a protein, and am unable to  
> figure out the correct tool to accomplish this:
> I have a protein and a region that I would like to replace with  
> another region.  Essentially, the insert is a long motif.   
> (Literally making a chimeric structure).   In Chimera, I can merge  
> the two pdb's at one terminus, however I can't seem to create the  
> bond at the other terminus, once the models are merged.  Is this  
> possible?

It should be.  Are you saying you don't know how to add the bond, or  
that the attempt to add the bond fails?

The simplest way to add the bond is to select the two atoms you want  
bonded and either type "bond sel" in Chimera's command line or use the  
"Adjust Bonds" tab of the Build Structure tool (in the Structure  
Editing category) to add the bond.  If these approaches fail for you,  
let me know what the error was exactly and I'll try to provide more  

> If not, does anyone know of  other programs out there that can  
> accomplish this, and any interest in putting it in chimera?

I hope it's already there!


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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