[Chimera-users] chemical structure

kotakis xristos kotakisx at yahoo.gr
Mon Apr 18 07:55:21 PDT 2016


Dear Dr. Meng,

thank you for your immediate and detailed reply.
it is greatly appreciated.
does your e-facility supports siRNA (short-interfering RNA) structures.
as you know siRNA have special biochemical features in comparison to common RNA molecules,
independently the sequence.
is there any specific option for siRNA and /or 
to add chemical modifications?

yours,
christos
--------------------------------------------
Στις Παρ., 15/04/16, ο/η Elaine Meng <meng at cgl.ucsf.edu> έγραψε:

 Θέμα: Re: [Chimera-users] chemical structure
 Προς: "kotakis xristos" <kotakisx at yahoo.gr>
 Κοιν.: chimera-users at cgl.ucsf.edu
 Ημερομηνία: Παρασκευή, 15 Απρίλιος 2016, 20:59
 
 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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