[Chimera-users] mRNA Structure

[Elaine Meng]

> On Dec 3, 2021, at 6:44 AM, SANDOVAL, KENNETH <K.SANDOVAL1 at nuigalway.ie> wrote:
> 
> Hello,
> I have a predicted secondary structure of an mRNA molecule. I am interested in trying to visualize this with UCSF Chimera. But I'm unsure what file format the program accepts for this? Does it need some sort of mRNA equivalent of a .pdb file?
> Thank you,
> Kenneth

Hello Kenneth,
The recommended address for Chimera questions is chimera-users at cgl.ucsf.edu CC'd here.

By secondary structure I'm guessing that you mean the base-pairing pattern, and not actually 3D atomic coordinates.  For Chimera you would generally need 3D atomic coordinates, most commonly in PDB format.

If that is really what you have (base-pairing information only), then here are two ideas for building a 3D structure in Chimera using that information:

(1) The RNArtist plugin to Chimera - quite extensive, has a lot of nice features, needs to be downloaded separately:
<https://github.com/fjossinet/RNArtist>
<https://www.rbvi.ucsf.edu/chimera/plugins/plugins.html>

(2) The "rna" command in Chimera can also build models but much more roughly.  See "rna model":
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#model>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco