[Chimera-users] rebuild DNA

[Damien Larivière]

Dear Elaine, Dear Marco

Many thanks for your message and suggestion.

Marco, I took contact with Xian-Jun Lu who is in charge of 3DNA. I'm 
waiting for his answer. I will give a feedback here.

Elaine, I keep in mind the idea of Maxsprout for protein rebuild from 
trace. About the DNA, since I have the initial DNA portion, not deformed 
and complete, I tried to make a morph between the complete DNA and its 
deformed trace. But only the trace of the original structure morphed.

A colleague is going to make something using Yasara. Wait and see.

Thanks

Damien

Le 14/04/2011 09:19, sette at uniroma2.it a écrit :
> May be you can try here
>
> http://rutchem.rutgers.edu/~xiangjun/3DNA/
>
> Marco
>
>
> 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
> University of Rome, "Tor Vergata"
> via della Ricerca Scientifica, 00133, Rome, Italy
> e-mail:        sette at uniroma2.it
> e-mail:        m77it at yahoo.it
> Tel.:          +39-0672594424
> Fax:           +39-0672594328
>
>
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