[Chimera-users] Build a quadruplex

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 25 10:58:27 PDT 2014


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
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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




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