Hi Ben/Jeff, Thank you for getting back to me. If I load an existing project/alignment, colour by conservation works. However, if in the same project I generate a new alignment from a set of fasta sequences, it doesn’t. The formatting of the new alignment is also different: lines are now wrapped and font type/size has changed.
Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK > On 17 May 2021, at 16:37, Geoffrey Barton (Staff) <g.j.bar...@dundee.ac.uk> > wrote: > > Hi Luca, > > Sorry you are having trouble with this. > > I just tried it with a Pfam alignment and it seemed to work OK for me both > conservation shading and group shading by conservation. > > I have the same version and macOS as you. Some things to try are: > reselect the colour by conservation option and select the “modify > conservation threshold” option as well. Sometimes selecting a different > colour scheme, then going back to clustalX/conservation colouring fixes > things. > > Mmm, are you talking about conservation on a linked structure? If so, I > will give that a try too. > > Geoff. > > -- > Geoff Barton FRSE FRSB | Professor of Bioinformatics | Head of Division of > Computational Biology > School of Life Sciences | University of Dundee | Scotland, UK | email: > g.j.bar...@dundee.ac.uk <mailto:g.j.bar...@dundee.ac.uk> > Web: www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk/> | twitter: > @gjbarton and @bartongrp > > > From: jalview-discuss-boun...@jalview.org > <mailto:jalview-discuss-boun...@jalview.org> > <jalview-discuss-boun...@jalview.org > <mailto:jalview-discuss-boun...@jalview.org>> on behalf of Luca Pellegrini > <lp...@cam.ac.uk <mailto:lp...@cam.ac.uk>> > Date: Monday, 17 May 2021 at 16:01 > To: Jalview-discuss@jalview.org <mailto:Jalview-discuss@jalview.org> > <Jalview-discuss@jalview.org <mailto:Jalview-discuss@jalview.org>> > Subject: [Jalview-discuss] Colour by conservation problem > > Hello, > > 'Colour by conservation’ with Clustal colouring has stopped working. Can > anyone please advise? I’m using Jalview v2.11.1.4 and macOS Catalina. > > Best wishes, > Luca > > Luca Pellegrini, PhD > Department of Biochemistry > University of Cambridge > Cambridge CB2 1GA > UK > > > > _______________________________________________ > Jalview-discuss mailing list > Jalview-discuss@jalview.org <mailto:Jalview-discuss@jalview.org> > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss > <http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss> > The University of Dundee is a registered Scottish Charity, No: SC015096
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