**
*Dear all,*
*
The PDBe team, in collaboration with David Sehnal (NCBR, Masaryk
University, Czech Republic), has developed a new data pipeline for
generating images of macromolecular structures. The new tool, PDBImages,
provides more consistent and scalable visualisation for a range of
different macromolecular views.
The PDBImages software is built using Mol* (https://molstar.org/viewer),
a powerful, open-source software for interactive molecular visualisation
in the browser. It leverages a 'headless' version of Mol*, enabling it
to render images directly from the command line without a graphical
interface. The use of Mol* provides many benefits to the pipeline,
including the ease in generating images of large structures and the
output of Mol* state files to enable interactive visualisation directly
within the browser.
PDBImages reads atomic XYZ coordinates from PDBx/mmCIF or binaryCIF
files and constructs predefined views of the macromolecular structures.
For each of these views it then outputs the following files:
*
Image files (PNG format)
*
Mol* state files - these allow replication of the view within the
Mol* viewer
*
Metadata files (JSON format)
If you are interested in using the PDBImages tool, it is available as an
npm package (https://www.npmjs.com/package/pdb-images
<https://www.npmjs.com/package/pdb-images>), with the code also
available on GitHub (https://github.com/PDBeurope/pdb-images
<https://github.com/PDBeurope/pdb-images>).
Read more:
https://www.ebi.ac.uk/pdbe/news/pdbimages-new-open-source-macromolecular-structure-imaging-pipeline
<https://www.ebi.ac.uk/pdbe/news/pdbimages-new-open-source-macromolecular-structure-imaging-pipeline>*
--
David Armstrong
Outreach and Training Lead
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
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