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.
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On 29/06/2018 01:01, Vonyx Crystal wrote:
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Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | [www.jalview.org](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)