[Jalview-discuss] Jalview Test Releases ! Help Wanted testing Jalview 2.11.1.0!

Dear jalviewers. Whilst everyone adjusts to restrictions due to the covid19 pandemic, we've been working on getting the next version of Jalview ready for release. If you would like to help out please read on ! Introducing the 'Jalview Test' application. Over the last 9 months, we have been t

[Jalview-discuss] Jalview 2.11.1.0 release and workshop next week

Dear Jalviewers, We're emailing to let you know about what's been happening over at www.jalview.org. The big news is that the latest release of Jalview - Version 2.11.1.0 is now available! In addition to some great new features, this release includes important fixes f

Re: [Jalview-discuss] jalview help needed

Hi Dimitris - The best place to ask for Jalview help is the Jalview discussion list: sign up at http://www.jalview.org/mailman/listinfo/jalview-discuss I've cced the list with my reply so others can benefit! On 07/05/2020 10:22, Dimitris Hatzopoulos wrote: Hope you are all well. Prompted to co

Re: [Jalview-discuss] problem with some features, windows 10 (hiDPI and Cygwin!)

Hello Maria On 14/07/2020 17:42, Maria D'Amato wrote: > */Select View⇒Feature settings/* > I don't see any list of features It may be that the sequences you are viewing do not have features available from the public databases. Also, if you loaded the sequences as a simple flat-file (e.g. fasta,

Re: [Jalview-discuss] How to change numbering on my alignment?

Hello Kate. Apologies for adding yet another response to Mungo's two suggestions. Your email suggests the 'Position 1' you talk about is position '1' of the alignemnt ruler, which counts columns rather than sequence positions. If one of your sequences is longer than the others, and there are n

Re: [Jalview-discuss] Custom or modified annotations

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 anno

[Jalview-discuss] Jalview patch release now available: Version 2.11.1.1

Dear Jalview Discuss ! We are pleased to announce that Jalview 2.11.1.1, the first patch release in the 2.11.1 series, is now available as an over the air update. You can also download standalone jars and the source for the new release via https://www.jalview.org/download This patch release in

Re: [Jalview-discuss] Help with colouring scheme and column selection

Hi Nicola - thanks for posting... it's a good question :) On 24/09/2020 11:19, Bordin, Nicola wrote: > My alignment consists of two sets of proteins, with conserved residues > columns for both datasets and various residues columns that are > conserved in one or or the other sub-alignment > > I’

Re: [Jalview-discuss] Color of percentage identity in Jalview

15 at 3:18 PM, James Procter <mailto:j.proc...@dundee.ac.uk>> wrote: Hello Israel. On 13/02/2015 11:20, Israel Hanukoglu wrote: I could not find a way to change the default color for percentage identity. The colouring for shading by percentage identity ca

[Jalview-discuss] Jalview 2.8 throws exception (was Re: Fw: jalview problem)

Hello Dharmender. You are using a fairly old version of Jalview - in fact, we released a bug fix for that version which should fix the error you have reported. You can download the installer for 2.8.0b1 here: http://www.jalview.org/old/v2_8_0b1/Web_Installers/InstData/MacOSX/NoVM/install-jalvi

Re: [Jalview-discuss] How to export the Consensus Logo?

Hello Natalia - are you using the JalviewLite applet or the desktop version ? In the desktop version, the File->Export Image option should let you export an EPS or SVG of your alignment view. Both will perfectly reproduce the logo, but you should make sure to tick the 'Lineart' option for rend

Re: [Jalview-discuss] Jalview: Problem with Colour/Percent identity

Thanks very much for your email Klara ! On 23/10/2016 02:41, Briknarova, Klara wrote: > I believe I encountered bug in the program. In the past (about a year or two > ago), I used Jalview to color a sequence alignment by percent identity. When > I tried again today (using Launch Jalview Desktop

Re: [Jalview-discuss] Jalview command line arguments

Hi Martina - JALVIEW_ANNOTATION is a tab separated file format - I think your file might have spaces instead. Try this one - you'll need to search/replace the '\t' with tab characters! JALVIEW_ANNOTATION # create a red box on any alignment from column 5 to 25 SEQUENCE_GROUP\trandom\t5\t25\t* PR

Re: [Jalview-discuss] version specific download links

Hello Martin. On 03/11/2017 12:00, Martin Raden wrote: > the current jalview download page only offers links to installers for > the latest version. > > In order to enable a stable install, are there any version specific > links available? Yes - http://www.jalview.org/development/Version-Archive

Re: [Jalview-discuss] version specific download links

Argh - sorry Kira - latency in my mail client... On 03/11/2017 12:01, Kira Mourao (Staff) wrote: > Hi Martin > > See the version archive at http://www.jalview.org/development/Version-Archive > > Best wishes > Kira > > On 03/11/2017, 12:00, "jalview-discuss-boun...@jalview.org on behalf of > Marti

[Jalview-discuss] JABAWS server down ? (Re: Jalview alignment issues)

Hi Julia - I'm just out of the office right now but I'm sure one of the Jalview team can help... On 02/02/2018 10:04, Julia Pedersen wrote: Hi Jim, I contacted you about a year ago regarding some issues with Jalview and I got excellent help with that (just in time for my half time thesis eval

Re: [Jalview-discuss] Jalview properties file : documentation ?

Hi Martin. On 20/02/2018 12:54, Martin Raden wrote: > is there some (online) documentation about the "properties file" that > can be set via the commandline arguments? Not exactly (I feel like I've written this before ;) ). There is source level documentation for what gets written to/read from th

Re: [Jalview-discuss] Jalview properties file : documentation ?

On 20/02/2018 20:27, Martin Raden wrote: .. now you got me. I eventually never opened the GUI so far! ;) the whole setup is done by a colleague and I am "only" responsible to get a backend pipeline working with his ideas. That's enough of a use case for us to run with! We do plan to have Jalvie

Re: [Jalview-discuss] Jalview properties file : documentation ?

On 21/02/2018 09:15, Mungo Carstairs (Staff) wrote: Though I notice another gui Preference, to specify a fixed id width, doesn't work: it is saved against "FIGURE_USERIDWIDTH", but the code looks for "FIGURE_FIXEDIDWIDTH" 😞. Sigh - thanks for lodging the bug https://issues.jalview.org/browse/

[Jalview-discuss] Jalview & Protein Structure and Function Prediction workshop: U. Liverpool - May 14-15th

Dear Jalview-Discuss ! If you haven't heard about it already, we'd like to let you know about a two day workshop that Jim and Suzanne will be running with Dan Rigden (one of our fabulous Scientific Advisory Board members!). The workshop is on 14-15th May at the University of Liverpool's Sherringt

[Jalview-discuss] Jalview 2.10.4b1 patch release

Dear Jalviewers! We've just released version 2.10.4b1 at www.jalview.org, and it will shortly also be available for install via bioconda. This patch release includes critical bug fixes for Uniprot sequence data retrieval, interactive SVG graphic export, and flatfile imp

Re: [Jalview-discuss] Sever Error! MUSCLE Web service in Jalview

Dear Gyppy Thanks so much for letting us know! It turned out the JABAWS server needed a restart - we'll do our best to make sure this doesn't happen again, but don't hesitate to let us know over twitter or here if you have any more problems ! Jim From: jalvie

Re: [Jalview-discuss] Colour by conservation problem

Hi Luca, Geoff, Ben and all on the list. I'm just posting the solution - Luca and I found for their problem: in Jalview 2.11.1.4 and previous versions, Colour By Conservation doesn't work when the Conservation annotation row isn't shown on the alignment, since it employs those results to modula

Re: [Jalview-discuss] Fwd: Color by secondary structure

Hi Roland & Vivek.. (& jalview discuss!) As Geoff says - please use the development build for this. We are just about to freeze the version for release, so it's "nearly" bug free! Please also follow Mungo's advice about configuring secondary structure processing in the 'Structures' preference

Re: [Jalview-discuss] Phosphorylation site prediction

Hi Nebosja - it looks like you might not have seen my reply to your earlier posting about this... maybe it went to spam ? Trying you direct just to make sure! You can see my (rather lengthy) reply in the archives here: http://www.jalview.org/pipermail/jalview-discuss/2018-October/001502.html

Re: [Jalview-discuss] can't download JalView

Hi Sha, I just saw this appear in our moderator list, since your email included images which were too big to post to jalview-discuss. Just to summarise: You're on windows 10. You had an issue with java, and after uninstalling/re-installing, Jalview didn't work. Uninstall/re-install lead to a s

[Jalview-discuss] retrieving reviewed sequences from Uniprot

Hi Asma - I'm just cc-ing Jalview discuss so others can find the answer to your question ! On 06/05/2019 13:18, AL-MURTADHA Asma wrote: when i open the box to fetch sequences from Uniprot, i want only to fetch the reviewed sequences, how can i do that. First make sure the 'ALL' option is selec

Re: [Jalview-discuss] Finding alignment and moving it to the top of the list

Hi Ahmad - just to add to Mungo here. On 27/05/2019 12:04, Mungo Carstairs (Staff) wrote: > Select | Find should highlight the next match of your search pattern in > the alignment which has focus. You may have fallen foul of a bug whereby > Find matched results in hidden regions. This is fixed in

Re: [Jalview-discuss] jalview with ubuntu 18.04

Thanks for the email, Maik! On 19/06/2019 09:35, Maik Engeholm wrote: I'm having a hard time getting Jalview installed/started under ubuntu 18.04. I have tried several things. Any suggestions how to proceed? Your help would be much appreciated. I can only apologise for the issues you've encou

Re: [Jalview-discuss] load annotations or future file

Hi Nail. Annotations from the PDBe-kb would be useful to others - we'd be happy to help you if you'd like to write a parser so Jalview could automatically import PDBe-kb annotation ! Jim. On 02/07/2019 09:48, Mungo Carstairs (Staff) wrote: > -

Re: [Jalview-discuss] Web services issue

!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 From: David Martin (Staff) Sent: 04 July 2019 10:41:39 To: jalview-discuss@jalview.org<mailto:jalview-discuss@jalview.org>; James Procter (Staff); Mungo

Re: [Jalview-discuss] 2D annotated map of secondary structures elements

Hi Ahmad. Did you see my previous reply ? http://www.jalview.org/pipermail/jalview-discuss/2019-August/001571.html As promised in my earlier email, I've also created a script to demonstrate how secondary structure elements could be automatically labelled: https://issues.jalview.org/secure/atta