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.

I would need the PDB file in order to see exactly what you mean here, and to fix the problem.

2.If I load the AMBER topology, the connectivity is correctly
recognized, but the first base and last are not connected by  the ribbon.

This problem is marked as "fixed" in our bug database, but some simple testing shows that it is not.  I have reopened that entry and will add you to the recipient list so that you will get notified when we fix it (hopefully for real!) again.

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu