Colour by conservation problem

Jalview Discussion
1

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

2

Hi Luca,

This should be working okay – I’ve just checked (using the PFAM (Seed) example) on macOS Big Sur and macOS Mojave, so hopefully Catalina which is in between is okay!

Can you send a sample project file for us to have a look at? If you’d prefer not to post to the list you can make an issue on https://issues.jalview.org/ and optionally give it a Security Level of “Sensitive” so it isn’t public.

One suggestion if you have any groups set in the alignment: make sure that you have ticked “Colour->Apply Colour to All Groups” to apply the Clustalx colouring to the groups (you may need to re-select “Colour->Clustalx” after that to make sure it gets applied to the groups), and when in the “Conservation Colour Increment” popup window make sure that the “Apply to all Groups” checkbox is checked.

If it’s not the groups thing, please let us know some more details so we can get to the bottom of it!

Best wishes,

Ben

···

From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Luca Pellegrini lp212@cam.ac.uk
Sent: 17 May 2021 15:30
To: Jalview-discuss@jalview.org 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
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

The University of Dundee is a registered Scottish Charity, No: SC015096

3

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.barton@dundee.ac.uk

Web: www.compbio.dundee.ac.uk | twitter: @gjbarton and @bartongrp

From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Luca Pellegrini lp212@cam.ac.uk
Date: Monday, 17 May 2021 at 16:01
To: Jalview-discuss@jalview.org 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
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

4

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.barton@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.barton@dundee.ac.uk <mailto:g.j.barton@dundee.ac.uk>
Web: www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk/&gt; | twitter: @gjbarton and @bartongrp

From: jalview-discuss-bounces@jalview.org <mailto:jalview-discuss-bounces@jalview.org> <jalview-discuss-bounces@jalview.org <mailto:jalview-discuss-bounces@jalview.org>> on behalf of Luca Pellegrini <lp212@cam.ac.uk <mailto:lp212@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
The University of Dundee is a registered Scottish Charity, No: SC015096

5

As an alternative, http://conseq.tau.ac.il does what you want. You can upload your MSA or it will generate one completely automatically. It colors the query sequence (conseq), or a 3D protein model (http://consurf.tau.ac.il). State of the art, robust, peer-reviewed algorithms, fully documented. Residues with large confidence intervals are colored yellow for caution.

Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his)
Univ. Massachusetts, Amherst – Martz.MolviZ.Org
Guided Exploration of Macromolecules with Powerpoint-Ready Animations: FirstGlance.Jmol.Org
Protein 3D Structure Wiki: Proteopedia.Org
Education: Biochem in 3D at MolviZ.Org
Find Functional Patches in Proteins: ConSurf.tau.ac.il
Atlas of Macromolecules: Atlas.MolviZ.Org
See multiple protein sequence alignments clearly: MSAReveal.Org
Pockets And Cavities Using Pseudoatoms in Proteins: PACUPP
Interactive Molecules in Architectural Spaces: MolecularPlayground.Org
Syllabi: Workshops.MolviZ.Org

···

On 5/17/21 10:30 AM, Luca Pellegrini wrote:

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)
6

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: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Luca Pellegrini lp212@cam.ac.uk
Sent: 17 May 2021 18:23
To: Geoffrey Barton (Staff) g.j.barton@dundee.ac.uk
Cc: Jalview-discuss@jalview.org Jalview-discuss@jalview.org
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) <g.j.barton@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.barton@dundee.ac.uk
Web: www.compbio.dundee.ac.uk | twitter: @gjbarton and @bartongrp

From: jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of Luca Pellegrini <lp212@cam.ac.uk>
Date: Monday, 17 May 2021 at 16:01
To: Jalview-discuss@jalview.org <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
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

7

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: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Luca Pellegrini lp212@cam.ac.uk
Sent: 17 May 2021 18:23
To: Geoffrey Barton (Staff) g.j.barton@dundee.ac.uk
Cc: Jalview-discuss@jalview.org Jalview-discuss@jalview.org
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) <g.j.barton@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.barton@dundee.ac.uk
Web: www.compbio.dundee.ac.uk | twitter: @gjbarton and @bartongrp

From: jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of Luca Pellegrini <lp212@cam.ac.uk>
Date: Monday, 17 May 2021 at 16:01
To: Jalview-discuss@jalview.org <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
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