Programmatic conversion of crystal structures into 3D printable files using Jmol

Vincent F. Scalfani, Antony J. Williams, Valery Tkachenko, Karen Karapetyan, Alexey Pshenichnov, Robert M. Hanson, Jahred M. Liddie, Jason E. Bara
  • Journal of Cheminformatics, November 2016, Springer Science + Business Media
  • DOI: 10.1186/s13321-016-0181-z

Open Data, Open Database and Open Source Code for 3D Printable Chemical Crystal Structures

What is it about?

Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Manual methods of converting crystal structures into 3D printable files are tedious. To overcome this limitation, we developed a programmatic method that allows for facile conversion of thousands of crystal structures directly into 3D printable files. The resulting 3D file dataset and Jmol 3D Print website will find wide use with researchers and educators seeking to 3D print chemical structures, while the scripts will be useful for programmatically converting large database collections of crystal structures into 3D printable files.

Why is it important?

This work provides direct access to a searchable website where chemists (and anyone else) can access 3D printable crystal structures that they can use to push to 3D printers. They don't have to worry about all of the tedious work involved with preparing the files for printing but take advantage of all of the work that has been done. Also the associated code is fully available for reuse and repurposing.

Perspectives

Dr Antony John Williams
United States Environmental Protection Agency

This article was almost three years in the making. The work was started while I was involved with the ChemSpider database and the intention was to host the data set in ChemSpider for public access but this never worked out. Finally we submitted the publication without the data set public except via FigShare (https://dx.doi.org/10.6084/m9.figshare.c.3302859.v6). However, the peer review process returned the not unexpected request that the data be made searchable. So, Bob Hanson went off and using his JMol expertise created a searchable website. For me this is the best example of the peer review process pushing on us as authors to produce a far superior publication and even better access to the data.

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http://dx.doi.org/10.1186/s13321-016-0181-z

The following have contributed to this page: Dr Antony John Williams and Prof. Jason E Bara