[Chimera-users] Build a quadruplex

sette at uniroma2.it sette at uniroma2.it
Thu Jun 26 11:02:25 PDT 2014

Hi Elaine,

this is very useful :)
Many thanks!!!

Elaine Meng <meng at cgl.ucsf.edu> ha scritto:

> Dear Marco,
> There is a "swapna" command for mutating nucleic acids:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html>
> The results may be fairly rough, with some nonoptimal geometries  
> and/or steric clashes, but you could try this and see if it meets  
> your needs.  There is also a Minimize Structure tool (in menu under  
> Tools... Structure Editing) or "minimize" command, but it has  
> limited ability to clean up a structure.
> 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
> On Jun 25, 2014, at 1:00 AM, sette at uniroma2.it wrote:
>> Dear all,
>> I'm interested to create a rough model of a quadruplex molecule  
>> using a specific sequence. One possibility could be to load a pdb  
>> structure of a quadruplex and « mutate » each nucleotide with the  
>> correct one. Is this feasible with Chimera ?
>> Alternative suggestions are appreciated as well.
>> Thanks for your help,
>> Marco

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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