Ah, yes, Jim. Looks like there are lots of possibilities here. Consider it
done. What do I need to do to get you what you need?
I opened Jalview, and loaded 2GIS; I don't see any interesting colors
there. (Let me work with you to implement Jmol 14.1 instead of Jmol 12.2.
There are a few issues because of the JavaScript refactoring, but nothing
too difficult.)
What you now have in Jmol is full control overall of any RNA secondary
structure selection. Let's put our heads together. Xiang-Jun has done an
incredible job of analyzing RNA secondary structure. You should consider
using this new x3dna web service. I think it is light-years ahead of
anything else out there, and it is an absolute joy to be working with him.
It took just five intense days to do all this. (And I have still 2 weeks
before I am off to my next adventure.)
I read at http://www.jalview.org:
*Jalview has built in DNA, RNA and protein sequence and structure
visualisation and analysis capabilities. It uses Jmol
<http://jmol.sourceforge.net/> to view 3D structures, and VARNA
<http://varna.lri.fr> to display RNA secondary structure. *
Perfect. Very nice.
and at
http://ndbserver.rutgers.edu/ndbmodule/services/download/rnamlview.html#4
*Next orientations *
- *add a 3D view panel interconnected with the 2D view*
Sounds like you are basically there already. No need for that!
And I see that you are just sending to VARNA the string that I am getting
as part of my x3dna DSSR summary, right? Very cool!
load =1bna/dssr
Secondary structures in dot-bracket notation (dbn) as a whole and per chain
>dssr-6Bzc2a nts=24 [whole]
CGCGAATTCGCG&CGCGAATTCGCG
((((((((((((&))))))))))))
>dssr-6Bzc2a-A #1 nts=12 [chain] DNA
CGCGAATTCGCG
((((((((((((
>dssr-6Bzc2a-B #2 nts=12 [chain] DNA
CGCGAATTCGCG
))))))))))))
BTW: VARNA needs to get signed properly; it is out of compliance and is
being blocked, I'm sure, by many many browsers. And I see you have used the
OpenSource signature as well in Jalview. What's your experience with that?
I wonder if the developers of VARNA would consider making its license GLPL
instead of GPL and allowing it to be a component of Jmol.
Bob
On Thu, Apr 10, 2014 at 4:26 AM, Jim Procter
<[email protected]>wrote:
> Hi Bob.
>
> I'm also interested, though I think you should be aiming big ;)
>
> The development build of Jalview (which will eventually be 2.8.2 by the
> summer) has an RNAView based secondary structure shading scheme that was
> developed by a summer student, Anne Menard, back in 2012. Currently,
> 2.8.2 uses Fabrice Jossinet's RNAView service to process the RNA chains,
> but it would be great if similar functionality were built in to Jmol,
> since Jalview 2.8.2 already uses DSSP assignments.
>
> Try loading PDB 2GIS into Jalview via its sequence fetcher, you can then
> open a Jmol view and a VARNA view, and also shade the sequence by RNA
> sugar edge interactions (Leontis/Westhoff/Hoogstein 2.5D annotation).
>
> Jim.
>
> On 09/04/2014 09:22, Angel Herráez wrote:
> > Bob and Xiang-Jun,
> >
> > That sounds VERY interesting!
> > Congratulations
> >
> > I will need some time before I can test this at some length.
> >
> > Yes, avoid the ribosome. I have a small set of PDB IDs that could be
> > used for testing/demo, if you need them -- tRNA, snall and large
> > rRNA, hairpins, an N base bound to a small RNA (riboswitch)...
> >
> > By the way, although this is separate, we recently had some problem
> > (while testing some Proteopedia issues) with individual nucleotides
> > (GMP, ATP...) being read as "nucleic" rather than "ligand". I
> > understand the rationale, but it is not ideal. That might also affect
> > when you start doing fancy nucleic secondary structure rendering.
> >
> >
> >
> >
> >
> >
> >
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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