Hi Francesco,

As Elaine mentions, as per the PDB standard the chain connectivity of standard residues (i.e. residues in ATOM records) is implied by their order in the file, barring TER records between the residues.  This is why Chimera is producing those longs bonds.  For example, your file has residues 300 and 301 one after the other in the PDB file without a TER card, so Chimera connects them despite them being >50A apart.  What you really need to do is reorder the file so that it is in connectivity order.

Also, the file was seemingly made by trjconv, which AFAIK is a program for converting Gromacs trajectories to PDB format.  I thought you were using an Amber trajectory.  Why aren't you using ambpdb, which directly converts Amber trajectories to PDB files?

Lastly, trjconv is doing a bad job with justification of hydrogen names in the 4 columns alloted to the atom name.  It does well with some names, like "1H2*" and " H3*" (so Chimera can deduce the element type from the first two columns) but then outputs some stinkers like " 1H7" and " 2H7".  Sigh.

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu

On Sep 23, 2010, at 11:31 AM, Elaine Meng wrote:

Hi Francesco,
Wow, this is a very pretty structure!  However, the PDB looks somewhat messed up.  Perhaps using the AMBER files solves most of these problems.

In PDB format, I believe the biopolymer (nucleic acid or protein) residues are connected by their order in the file, unless a break is enforced with TER.  However, the order in this PDB file seems to be quite different than what it should be, for the correct connectivity.  Residue 75 is very far from 76, 150 is very far from 151, etc. every 75 positions.  I tried just putting TER after every 75 residues, which does eliminate the very long bonds.  However, it seems like there may be other bonds that are supposed to be there that are not, and it would be necessary to do a lot of reorganization and renumbering of residues in this file to get the correct connectivity.  For example, it looks like maybe 76 is really supposed to be connected to 150, 75 is really supposed to be connected to 1, etc.

If there were correct ordering in the PDB file (and maybe this is already true for when you use the AMBER files as input), the Chimera limitation would give you just one break in each circular strand.  If this DNA is all one big circular strand, there should be only one break in the ribbon.
Best,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco



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