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Sorry, forgot to copy the list…
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Hi Roland,
Jim Procter will be able to give the definitive answer if I miss anything, but you can certainly do this in the current development version (which will be the release version very soon…) You can download this from the “Development” page - I usually select the Webstart 2G version.
First download the sequences for your PDB structures: File->Fetch Sequences then PDB. You can search PDBe with various criteria to select structures you want.
Once they are in Jalview goto Colour->By Annotation and choose secondary structure. tick the “Per-sequence only” box.
Now go to the View->Feature Settings and toggle off the default colouring.
The secondary structure should appear on the sequence alignment as coloured blocks. If you don’t want the arrows and cylinders under the alignment you can turn these off either individually or as a block.
I think this is a common thing to do so in future releases we’ll likely tweak the user interface to make it easier.
I hope this helps.
Geoff.
Hello,
Is it possible to color every sequence in an alignment by experimental secondary structure for those sequences that have structures in the PDB?
Can I do this automatically or alternatively, can I import a file of secondary structure assignments (that I can create) that would indicate what residues to color in each sequence? I want to color each sequence differently according to whatever its secondary structure is in its experimental structure.
It would be terrific if Jalview could look up structures in the PDB (which it currently does) and then color the sequence in the alignment by the experimental secondary structure annotated in the PDB files.
Thanks,
Roland
Roland Dunbrack
Professor, Institute for Cancer Research
Fox Chase Cancer Center
Philadelphia PA 19111
http://dunbrack.fccc.edu
http://dunbrack.org_______________________________________________ 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)
Subject: Re: [Jalview-discuss] Fwd: Color by secondary structure
Date: Wed, 5 Oct 2016 09:25:41 +0100
From: Geoff Barton gjbarton@dundee.ac.uk
Reply-To: gjbarton@dundee.ac.uk
Organisation: University of Dundee
To: Roland Dunbrack roland.dunbrack@gmail.com
On 05/10/2016 00:11, Roland Dunbrack wrote:
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Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk)
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
The University of Dundee is registered Scottish charity: No.SC015096