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 modulate the alignment's shading.
If you need to apply colour by conservation and the conservation row isn't visible, its most likely that you disabled the conservation calculation in your Jalview Preferences. To re-enable you will need to open the preferences dialog and make sure both consensus and conservation calculations are enabled in the 'Visual' tab. This only applies to newly opened alignments, so you'll need to reopen the file you imported, or press the 'New Window' button on the alignment service job you just imported. hope that helps ! jim. ________________________________ From: [email protected] <[email protected]> on behalf of Luca Pellegrini <[email protected]> Sent: 17 May 2021 18:23 To: Geoffrey Barton (Staff) <[email protected]> Cc: [email protected] <[email protected]> Subject: Re: [Jalview-discuss] Colour by conservation problem 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) <[email protected]<mailto:[email protected]>> 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: [email protected]<mailto:[email protected]> Web: www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> | twitter: @gjbarton and @bartongrp From: [email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> on behalf of Luca Pellegrini <[email protected]<mailto:[email protected]>> Date: Monday, 17 May 2021 at 16:01 To: [email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> 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 [email protected]<mailto:[email protected]> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss The University of Dundee is a registered Scottish Charity, No: SC015096 The University of Dundee is a registered Scottish Charity, No: SC015096
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