Dear Heather, thanks for posting ! On 16/09/2020 22:04, Heather E. Driscoll wrote: > I have been using the alpha helix and beta sheets annotation function in > Jalview to label a genome alignment with protein names at the bottom of > the MSA. Is there a way to modify the colors and of these annotations?
Unfortunately not currently, but you've raised a good case for doing it. We'll hopefully be adding new annotation row functionality for release in early 2021.. we'll try and fit this in ! (you can sign up on our bug tracker and hit the 'Watch' button to get updates on the issue here https://issues.jalview.org/browse/JAL-3752). > Ideally, I'd use the alpha helix shape since it doesn't have the beta > sheet arrow. Is this a possibility? Or is there another way to > accomplish the task? Any help you may provide is appreciated. Right now, the only thing I can suggest is a workaround. You can use a jalview annotation file to add an additional 'BAR_GRAPH' annotation row which is all '0' except where genes occur (add a 1 instead). You can then also specify each bar's colour to achieve the effect you want, albeit in a clumsy fashion. I'm sure you've seen it, but the documentation for creating Jalview annotation files is here: http://www.jalview.org/help/html/features/annotationsFormat.html#annrows Jim. PS. You can configure the symbol shown below each histogram as well, so you don't actually see the values creating the bar! -- ------------------------------------------------------------------- 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 | www.compbio.dundee.ac.uk _______________________________________________ Jalview-discuss mailing list Jalview-discuss@jalview.org http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
