Visualisation of chemical data. Use cases for publication of crystal structures. Brian McMahon Research & Development Officer International Union of Crystallography 5 Abbey Square Chester CH1 2HU email@example.com. DataCite Summer Meeting, Hannover 7-8 June 2010.
Use cases for publication of crystal structures
Research & Development Officer
International Union of Crystallography
5 Abbey Square
Chester CH1 2HU
DataCite Summer Meeting, Hannover
7-8 June 2010
(image plate, diffractometer, film)
(six-dimensional structural model)
Every structural paper has an associated data set (CIF)
These are free to access, even for subscription journals
Hence accessible from browsable Table of Contents (as well as from article)
User can download CIF data set directly
Or visualise the structure interactively in three dimensions
... using a standard view supplied by a visualisation applet (Jmol) ...
... or a 'helper' application of the reader's choosing (Mercury)
IUCr journals provide an authoring toolkit for creating enhanced figures –
Data visualisations crafted by the author (but allowing the reader to interact fully with the data and create other visualisations if desired)
The enhanced figure will appear (with caption) as a normal figure in the online journal; the PDF/print editions will have an equivalent static view.
Additional views and interactive features can be added by the author if desired.
The structural data (CIF) can be uploaded to the journal production office ...
... from the user's hard drive (as part of the article submission process) ...
... from an external database using a known accession code (e.g. dn3141 for Crystallography Journals Online, 3dez for Protein Data Bank) ...
... or from a registered data DOI (e.g. 10.2210/pdb3dez/pdb)
Article in IUCr Crystallography Journals Online
Macromolecular structure from Protein Data Bank
Crystal structure in U. Southampton eCrystals repository
Unilever Cambridge Centre for Molecular Informatics / Project XYZ
* Need consistent protocols for retrieving data set from larger data collection