Programmatic conversion of crystal structures into 3D printable files using Jmol
| Autor: | Robert M. Hanson, Vincent F. Scalfani, Jahred Liddie, Valery Tkachenko, Alexey Pshenichnov, Karen Karapetyan, Jason E. Bara, Antony J. Williams |
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| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Nanotechnology Library and Information Sciences computer.software_genre Crystals JSmol 03 medical and health sciences Data file Physical and Theoretical Chemistry Visualization 3d print Crystallography Database Open data 05 social sciences Methodology 050301 education 3D printing computer.file_format File format Computer Graphics and Computer-Aided Design Computer Science Applications Crystallographic Information File 030104 developmental biology Scripting language VRML ComputingMethodologies_DOCUMENTANDTEXTPROCESSING Crystallography Open Database Jmol 0503 education computer Dataset |
| Zdroj: | Journal of Cheminformatics |
| ISSN: | 1758-2946 |
| DOI: | 10.1186/s13321-016-0181-z |
| Popis: | Background Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and 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. Results A collection of over 30,000 crystal structures in crystallographic information file (CIF) format from the Crystallography Open Database (COD) were programmatically converted into 3D printable files (VRML format) using Jmol scripting. The resulting data file conversion of the 30,000 CIFs proceeded as expected, however some inconsistencies and unintended results were observed with co-crystallized structures, racemic mixtures, and structures with large counterions that led to 3D printable files not containing the desired chemical structure. Potential solutions to these challenges are considered and discussed. Further, a searchable Jmol 3D Print website was created that allows users to both discover the 3D file dataset created in this work and create custom 3D printable files for any structure in the COD. Conclusions Over 30,000 crystal structures were programmatically converted into 3D printable files, allowing users to have quick access to a sizable collection of 3D printable crystal structures. Further, any crystal structure (>350,000) in the COD can now be conveniently converted into 3D printable file formats using the Jmol 3D Print website created in this work. The 3D Print website also allows users to convert their own CIFs into 3D printable files. 3D file data, scripts, and the Jmol 3D Print website are provided openly to the community in an effort to promote discovery and use of 3D printable crystal structures. The 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. |
| Databáze: | OpenAIRE |
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