[Jmol-users] RNA/DNA Secondary Structure, anyone?

Hi Bob.

I'm also interested, though I think you should be aiming big :wink:

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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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?

read on :slight_smile:

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.)

Happy for that to happen! I was putting off the jump to 14 until I had 2.8.1 out the door (it has been a very long time coming!), and our next server backend release (Jabaws 2.1) rolled out.

Basically, however, in 2.8.2, because I’m using Jmol’s data model to parse PDB data, we’ll finally be able to share selections across Jmol & Jalview. There are some user experience choice points that need looking at, but programmatically it should be straightforward. That means it’ll also be easy to grab secondary structure from Xiang-Jun’s DSSR if it gets housed in the Jmol datamodel. The biggest issue is making sure Jalview reliably catches any Jmol data events and updates its own model.

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.)

:slight_smile: I hear you’ll be off to EBI in a few months - too! I’ll try to drop by in July!

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 to view 3D structures, and VARNA to display RNA secondary structure.

VARNA integration is still a bit flaky. Something I want to work on more in the 2.8.2 beta period. At the moment, we aren’t storing/restoring VARNA layouts in Jalview projects, and that’s kind of essential :slight_smile:

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!

Pretty much ! However, we need a bit more sophistication to enable bidirectional interactive editing - which is something that Jan Engelhart - who did the original integration back in 2012, was really interested in!

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
))))))))))))

this actually presents an interesting problem with Jalview - it treats each chain as a single row in the alignment, and doesn’t understand (yet) connections between chains. That’s where dedicated RNA/DNA tools like Assemble do way better, because they show an alignment for each side of the base pair network… slightly confusing but very powerful once you get your head around it!

BTW: VARNA needs to get signed properly; it is out of compliance and is being blocked, I’m sure, by many many browsers.

yep. I’ve forwarded your email to Yann - of course, people could use the one that I resign for Jalview’s use, but it’d be better if varna’s home build was fixed :slight_smile:

And I see you have used the OpenSource signature as well in Jalview. What’s your experience with that?

Pretty good actually - I try to minimise infrastructure costs as far as possible, and was pretty unhappy about the change in requirements. Whilst the various communities that use our tools could be organised enough to start their own trust network, the changes in default security on OSX pretty much make it a requirement to pay something to avoid confusing security (non)warnings. As far as I know, no one has yet complained about the certificate being confusing and not trusted, but we are keeping an eye on our launch stats to see if people are being put off by the slightly weird Author text that certum.pl insert in their free certificates.

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.

again - I have to leave it to Yann to answer that one :wink:

I’m flat out at the moment, but will get back to you next week re 12-14. If you want commit rights, then sign up over at issues.jalview.org and I’ll add them to your profile ! Git access is via https://source.jalview.org/git/jalview.git

Jim.

···

Thanks for your interest Bob - lets see how far we can go !

On 10/04/2014 13:26, Robert Hanson wrote: