[Chimera-users] ribbon display of circular DNA structures

Eric Pettersen pett at cgl.ucsf.edu
Mon Sep 26 15:58:42 PDT 2011

On Sep 26, 2011, at 1:05 PM, jens j birktoft wrote:

> Hi Everybody
> How can I display a circular DNA structure with three helices  
> without a break at the places where the ends meet according to the  
> numbering system.  In the real structure there is no break in the  
> covalent structure

Hi Jens,
	If you are using a PDB file, there needs to be a CONECT record in the  
file indicating the two atoms that are bonded between the first and  
last residues.  Without that bond, any ribbon depiction will not join  
those residues.  Also, cyclic structures did not have proper ribbon  
representation before the 1.5.3 release, in case you are using an old  
version of Chimera.
	One reasonably easy way to establish that CONECT record if it's  
missing is to open the structure in Chimera, select the two atoms, and  
type "bond sel" in the command line (Favorites->Command Line), then  
write out a new PDB.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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