[Jalview-discuss] RNA Secondary Structure Annotation bug

[Jim Procter]

Hi Vaish - thanks for taking the time to post this.. it is very much a
bug, due to an inconsistency between the stockholm and annotationfile
parsers when it comes to RNA secondary structure.

I've created an issue for it here:
https://issues.jalview.org/browse/JAL-3053

Firstly, Jalview should be handling the stockholm file correctly, but
I'm curious about whether you consider it essential to see the type of
bracket for each helix in the secondary structure line ?  In fact -
that's the main difference, because in the Annotation file, Jalview
recognises that there is a secondary structure in the row and disables
the display of the brackets, but we could always make that optional...

Jim.

Good day,
Jalview is being inconsistent in reading in the secondary structure
for RNA alignments. Attached is an alignment file. When Jalview opens
it, the "Secondary Structure" Annotation row is colored orange,
indicating that there is a problem with the annotation.
Jalview is unable to display any colours in the alignment with the RNA
Helices option.
We found a convoluted solution to the problem. 
First, you export the Secondary Structure annotation by right clicking
on the annotation row, and save it to a file. 
Then, you re-import the exported annotation file using the File> Load
Features/Annotations menu item. And then you can color the RNA helices.
However, it seems like Jalview is treating the annotation row as a
protein structure, and not an RNA helix structure, and we are unable
to see the brackets, which were formatted as an Extended Dot-Bracket
Notation according to ViennaRNA
Saving this alignment then reopening it with Jalview returns us to
square one again.
Upon comparing the two different annotation rows with a text editor,
we were unable to find a difference between the old SS row and the new
SS row, and the stockholm file looks correct, even before the fix.
How can we avoid this problem with our secondary structure?
Thank you,
Vaish