[Chimera-users] ribbon display of circular DNA structures
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
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.
UCSF Computer Graphics Lab
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