[Chimera-users] Build a quadruplex

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 26 11:27:18 PDT 2014


You're welcome!

I forgot to mention that for RNA (not DNA), there is a nice modeling/refinement plugin, Assemble2, developed by Fabrice Jossinet at University of Strasbourg:

<http://bioinformatics.org/assemble/index.html>

It interfaces with web services for RNA structure prediction and refinement.

Elaine


On Jun 26, 2014, at 11:02 AM, sette at uniroma2.it wrote:

> Hi Elaine,
> 
> this is very useful :)
> Many thanks!!!
> Marco
> 
> 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.
>> 
>> 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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