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
Best
Jens
*+++++++++++++++++++++++++++++++++++++++++++++++++++++++* * * *Jens J. Birktoft New York University, Department of Chemistry. **e-mail: jb160@nyu.edu jens.knold@gmail.com **Phone: 212-749-5057 *
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
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
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