Thanks for your interest Bob - lets see how far we can go !
On 10/04/2014 13:26, Robert Hanson wrote:
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 :)
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.)
:) 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
<http://jmol.sourceforge.net/> to view 3D structures, and VARNA
<http://varna.lri.fr> 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 :)
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 :)
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 ;)
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.
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