[Chimera-users] ribbon problem

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 23 09:19:09 PDT 2010

Hi Francesco,
It is difficult to try anything without the files.  Here are some generalities.

Usually bonds can be specified correctly in PDB by following the format rules and using CONECT lines if needed.  However, the format rules might not include the situation of a circular biopolymer.   Similarly, I believe the ribbon code is not designed to consider a circular chain (tested on 2kux, cyclic peptide).

Any extra bonds can just be deleted in Chimera, say using the "Adjust Bonds"  tab in the "Build Structure" tool, or the command ~bond, but this would not fix the ribbon problem.
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 23, 2010, at 6:33 AM, Francesco Oteri wrote:

> Dear all,
> I'd like to use chimera to do a picture of a circular DNA with ribbon 
> representation.
> I found the two following problems:
> 1.If I load the .pdb files, chimera is unable to recognize the topology 
> and shows extra-bond connecting the last base of a strand with the 
> previous of the other strand.
> 2.If I load the AMBER topology, the connectivity is correctly 
> recognized, but the first base and last are not connected by  the ribbon.
> Is there any solution?
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