[Chimera-users] chemical structure

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 15 10:59:55 PDT 2016


Dear Dr. Christos Kotakis,
You probably meant PDB (not PDF), which you can save from the Chimera File menu or with the “write” command after creating the structure.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>

To create the structure in Chimera, I can think of 3 general ways:

(1) for a completely regular, idealized double helix, you can use Build Structure (in menu under Tools… Structure Editing), the Start Structure section, open “helical DNA/RNA”, choose “RNA,” enter sequence, etc.  However, if there are unpaired bases on the ends or you expect the structure should be irregular rather than a perfect helix, you may need to use one of the other methods.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start>

(2) there is an “Assemble2” plugin to Chimera that does all kinds of RNA structural modeling.  It is quite fancy… one can draw the 2D diagram of the desired RNA and then calculate possible 3D structures.  You have to get the plugin separately from
<http://bioinformatics.org/assemble/index.html>
<http://www.bioinformatics.org/assemble/downloads.html>

(3) if there is a 3D structure already available for a similar siRNA duplex (i.e., you expect your duplex to have similar 3D structure), you can open that structure in Chimera and then try “mutating” the bases to your sequence with the “swapna” command.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html>

I hope this helps,
Elaline
-----
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 15, 2016, at 9:15 AM, kotakis xristos <kotakisx at yahoo.gr> wrote:

> Dear Sir/Madam,
> I have a siRNA duplex (21nt) of a given sequence
> and I would like to generate the chemical structure of that in a single file
> (e.g. pdf)
> 
> What do you suggest?
> 
> looking forward to your response
> thanks in advance,
> yours,
> Dr. Christos Kotakis
> _



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