[Chimera-users] rebuild DNA

sette at uniroma2.it sette at uniroma2.it
Thu Apr 14 00:19:00 PDT 2011

May be you can try here



Def. Quota "Elaine Meng" <meng at cgl.ucsf.edu>:

> 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.
> <http://structure.usc.edu/make-na/>
> <http://www.ebi.ac.uk/Tools/maxsprout/>
> Sorry I couldn't help more -- maybe someone else on the list will  
> know of a suitable program.
> Elaine
> -----
> 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
>> <DNAdeformed.pdb>_______________________________________________
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Dr.Marco Sette, Ph.D.

Department of Chemical Sciences and Technology
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