[Chimera-users] rebuild DNA

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 13 10:23:48 PDT 2011

Dear Damien,
Sorry, Chimera does not have automated methods for building all-atom models from chain traces, either protein or DNA.  Chimera's Build Structure tool (under Tools... Structure Editing) enables manual, step-by-step building, but it is not guided by an input backbone trace, and it would be far too tedious for such long chains anyway.

I haven't done much building in other programs, but I try to keep track of useful web servers.
For protein CA traces, there is a Maxsprout server, but for nucleic acid building, I only know of one web server (make-na) and I believe it just builds the whole thing from scratch and cannot be guided by a chain trace.


Sorry I couldn't help more -- maybe someone else on the list will know of a suitable program.
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 13, 2011, at 9:46 AM, Damien Larivière wrote:

> Dear all,
> Here is a PDB file of a DNA portion. It contains only the atoms of the backbone chain trace.
> Is there a way to rebuild the remaining parts (sugar,...)?
> Many thanks for your help
> Damien
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