[Chimera-users] Curves+ graphics of DNA

[Elaine Meng]

Hi Richard, 
It is a format problem -- compared to "standard" PDB,  the discrepancies are that the residue names are too long, multiple atoms in the same residue have the same name, and the atom names (unless 4 characters) should start one column later.  However, these are not why you are getting connections...  there will be an attempt to connect atoms within the same residue (having the same residue number), as well as successive-in-the-file ATOM residues that are not separated by TER.  I believe you will get the expected result by either changing "ATOM  " to "HETATM" or by putting a TER between the residues (both alternatives attached).

I hope this helps,
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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On Dec 21, 2010, at 6:42 AM, Richard LAVERY wrote:

> I am trying to visualize the graphic output from the Curves+ of a DNA duplex, which consists of two smooth backbone traces linked by vectors indicating the measured widths of the minor and major grooves. In the test case shown, adding two atoms defining one such vector and a single CONECT line linking them together (see attached PDB file) leads to three new bond vectors in the representation shown below. Am I making a mistake, or is this a problem with Chimera?
> 
> Richard LAVERY
> richard.lavery at ibcp.fr
> http://web.mac.com/laveryr/Homepage
> 
> Institut de Biologie et Chimie des Prot?ines
> 7 passage du Vercors, Lyon 69367, France
> Tel:  +33 (0)4 72 72 26 37, Cell 06 62 76 84 47