Hi Luca, Thanks for the extra information. I'm not sure about the different formatting (although have a theory!), but I have another suggestion about the Colour by conservation.
If you aren't closing the "Conservation Colour Increment" popup window (with the percentage slider) between adjusting the first alignment window, and adjusting the second, then the slider will stay associated with the first alignment window. It's possible to get to a state where both alignment windows have the "Colour->By Conservation" option ticked, but the slider is only ever associated with one of them! If you select "Colour->By Conservation" in the new alignment window (if it's already ticked, you may need to select it once to untick it and then select it again) then that should ensure the slider popup is associated with that alignment, and will hopefully adjust the colouring accordingly in the expected window. Be sure that "Colour->Clustalx" is selected in that window first too! Let us know if this does or doesn't help. Best wishes, Ben ________________________________ 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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