Scalfani Vincent F, Williams Antony J, Tkachenko Valery, Karapetyan Karen, Pshenichnov Alexey, Hanson Robert M, Liddie Jahred M, Bara Jason E
University Libraries, Rodgers Library for Science and Engineering, The University of Alabama, Tuscaloosa, AL 35487 USA.
ChemConnector, 513 Chestnut Grove Court, Wake Forest, NC 27587 USA.
J Cheminform. 2016 Nov 23;8:66. doi: 10.1186/s13321-016-0181-z. eCollection 2016.
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.
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.
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.
三维（3D）打印晶体结构对化学教学和研究很有用。当前将晶体结构转换为3D可打印文件的手动方法既耗时又繁琐。为克服这一局限，我们开发了一种程序化方法，可将数千个晶体结构直接轻松转换为3D可打印文件。
使用Jmol脚本，将来自晶体学开放数据库（COD）的30000多个晶体学信息文件（CIF）格式的晶体结构集合程序化转换为3D可打印文件（VRML格式）。30000个CIF的数据文件转换按预期进行，然而，在共结晶结构、外消旋混合物以及带有大抗衡离子的结构中观察到了一些不一致和意外结果，导致3D可打印文件不包含所需的化学结构。本文考虑并讨论了应对这些挑战的潜在解决方案。此外，还创建了一个可搜索的Jmol 3D打印网站，用户既能发现本研究中创建的3D文件数据集，也能为COD中的任何结构创建自定义3D可打印文件。
超过30000个晶体结构被程序化转换为3D可打印文件，使用户能够快速访问大量的3D可打印晶体结构集合。此外，现在可以使用本研究中创建的Jmol 3D打印网站，将COD中的任何晶体结构（超过35万个）方便地转换为3D可打印文件格式。3D打印网站还允许用户将自己的CIF转换为3D可打印文件。3D文件数据、脚本以及Jmol 3D打印网站已向社区公开提供，以促进3D可打印晶体结构的发现和使用。3D文件数据集和Jmol 3D打印网站将在寻求3D打印化学结构的研究人员和教育工作者中得到广泛应用，而脚本将有助于将大量晶体结构数据库集合程序化转换为3D可打印文件。
