Just a detail, but you also need to ensure that in Tools | Preferences, under Structure, the options
- Process secondary structure from PDB - Add secondary structure annotation to alignment are selected (and add Temperature Factor if of interest). Mungo Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> ________________________________ From: jalview-discuss-boun...@jalview.org <jalview-discuss-boun...@jalview.org> on behalf of Geoff Barton <gjbar...@dundee.ac.uk> Sent: 05 October 2016 09:26:09 To: Jalview-discuss@jalview.org Subject: [Jalview-discuss] Fwd: Re: Fwd: Color by secondary structure Sorry, forgot to copy the list.. -------- Forwarded Message -------- Subject: Re: [Jalview-discuss] Fwd: Color by secondary structure Date: Wed, 5 Oct 2016 09:25:41 +0100 From: Geoff Barton <gjbar...@dundee.ac.uk><mailto:gjbar...@dundee.ac.uk> Reply-To: gjbar...@dundee.ac.uk<mailto:gjbar...@dundee.ac.uk> Organisation: University of Dundee To: Roland Dunbrack <roland.dunbr...@gmail.com><mailto:roland.dunbr...@gmail.com> 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. On 05/10/2016 00:11, Roland Dunbrack wrote: 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 -- Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology School of Life Sciences | University of Dundee, Scotland, UK | g.j.bar...@dundee.ac.uk<mailto:g.j.bar...@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 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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