[Chimera-users] chemical structure

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 18 16:44:32 PDT 2016

Dear Christos,
Nothing specifically, but you could either

(1) use Build Structure, the Modify Structure section to manually build atom-by-atom
(2) superimpose modified bases from other crystal structures onto the corresponding positions in your structure, write out the superimposed coordinates (File… Save PDB, “relative to” your structure), then manually in a text-editor (not in Chimera) substitute the coordinates of the atoms from the modified base for the unmodified base in your PDB file.

Both of these require a fair amount of manual labor and are not easy or simple.  

Maybe the Assemble2 plugin has some features for building these modified bases, but I haven’t tried it, so I’m not sure.  You would have to check the manual for that plugin.
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 18, 2016, at 7:55 AM, kotakis xristos <kotakisx at yahoo.gr> wrote:
> 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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