[Chimera-users] DNA Ribbon

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 18 18:15:49 PST 2012

If you open a "standard" PDB file of DNA (such as from the RCSB Protein Data Bank, www.rcsb.org) in Chimera, it will automatically be shown with ribbons.  However, I'm guessing the problem in your case is that the DNA structure from Spartan has different atom and residue names, or maybe it is all one big residue, so it is not recognized as DNA. Unfortunately the only way I can think of to fix that problem is to text-edit the file to use standard atom and residue names, and that may be difficult.

You would have to look at a standard PDB file of DNA or the chemical component pages at the RCSB Protein Data Bank to find out the standard naming system.

Assuming it is possible to fix up your file, you may want to take a look at some tutorials.  These include viewing DNA as ribbons and showing the bases with a few different styles.

... with menu and GUIs

... or with commands

Sorry I don't have a better (easier) solution.
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 18, 2012, at 2:42 PM, Yoshus Kumka wrote:

> Hello,
> Does anyone know how to assign ribbon attributes to DNA... So I created a stretch of DNA in Spartan and converted the file to pdb which does not contain any attributes such as helical information to automatically have chimera show backbone as a ribbon... 
> I would like to display the DNA backbone as a ribbon and show the bases... But I don't know how to assign the backbone atoms a ribbon property... Please help

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