[Chimera-users] chemical structure
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?
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
You probably meant PDB (not PDF),
which you can save from the Chimera File menu or with the
“write” command after creating the structure.
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
(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
(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.
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab
(Chimera team) and Babbitt Lab
California, San Francisco
Apr 15, 2016, at 9:15 AM, kotakis xristos <kotakisx at yahoo.gr>
> 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,
> Dr. Christos Kotakis
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