PDB sequence naming

Shall I comment out lines 178-179 of ws.dbsources.Pdb?

That would mean getting a sequence name like

4WV3|A

instead of

PDB>4wv3|4WV3|A

or do we want the half-way house

PDB>4WV3|A

mungo

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

···

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
www.compbio.dundee.ac.uk

The halfway house is, strictly speaking, the valid choice.

If we are really brave and drop the database name prefix then we should also do it for all the other dbsources (Ensembl, Uniprot, EMBL, etc). I think we should be brave OutlookEmoji-😝.png!

See: http://issues.jalview.org/browse/JAL-2203

···

From: jalview-dev-bounces@jalview.org jalview-dev-bounces@jalview.org on behalf of Mungo Carstairs (Staff) g.m.carstairs@dundee.ac.uk
Sent: 16 September 2016 12:33:00
To: jalview-dev@jalview.org
Subject: [Jalview-dev] PDB sequence naming

Shall I comment out lines 178-179 of ws.dbsources.Pdb?

That would mean getting a sequence name like

4WV3|A

instead of

PDB|4wv3|4WV3|A

or do we want the half-way house

PDB|4WV3|A

mungo

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

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

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
www.compbio.dundee.ac.uk