how can I stop ongoing alignment

Hi Rob. Thanks for the email - we don't allow bulky attachments so I'm
just replying directly on list.

I've been making an alignment and got some secondary structure
prediction (not very good though) via RNAalifold.


But even after
unticking the alignment box (under Webservice/sec.struc prediction)
the requests for JABA keep going on, despite having been off-line and
gone through a couple of sleep/resume cycles.

Ah. I've seen this happen when the RNAAliFold job didn't complete for
some reason. Jalview is supposed to deal with this gracefully, but if
its due to a network problem (like you sleeping the computer), then it
may have given up and lost track of the computation.

Does anyone have a clue

how one can actively kill these processes without having to quit the
program or close the file....?

The easiest way would be to save everything as a Jalview project
(Desktop's File -> Save Project menu option), and then load that project
into another copy of Jalview.

If you can reproduce the problem with RNAAliFold, please let us know !

ps. feel free to recommend any way we might improve the RNA secondary
structure prediction services on offer !


On 31/05/2016 10:00, rob van nues wrote:

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 | |