[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
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>
or
(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.
Best,
Elaine
----------
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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