Scalfani et al. J Cheminform (2016) 8:66 DOI 10.1186/s13321-016-0181-z METHODOLOGY Open Access Programmatic conversion of crystal structures into 3D printable files using Jmol Vincent F. Scalfani1*, Antony J. Williams2*, Valery Tkachenko3, Karen Karapetyan3, Alexey Pshenichnov3, Robert M. Hanson4, Jahred M. Liddie5 and Jason E. Bara5 Abstract 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 Crystal- lography 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 cre- ated 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 convert- ing large database collections of crystal structures into 3D printable files. Keywords: 3D printing, Dataset, Jmol, JSmol, Crystals, Crystallography, Visualization, Open data Background structures that would be difficult or impossible to create Three-dimensional (3D) printed crystal structures offer with traditional molecular model fabrication techniques several advantages over traditional molecular model con- [1]. As such, numerous researchers have recently used 3D structs (e.g. plastic molecular model kits, Styrofoam balls, printed crystal structures to advance their teaching and beads). Perhaps the greatest advantage is that 3D print- research [1–7]. ing is capable of fabricating extremely complex molecular Digital 3D printable crystal structure files can be man- ually created from standard crystallographic information files (CIF) using a variety of open source, free, and com- *Correspondence: [email protected]; [email protected] mercial software packages [1, 2, 4–6]. In general, the crys- 1 University Libraries, Rodgers Library for Science and Engineering, The University of Alabama, Tuscaloosa, AL 35487, USA tal structure is first opened in a crystallographic viewing 2 ChemConnector, 513 Chestnut Grove Court, Wake Forest, NC 27587, program [8–12] where the structure representation is USA adjusted to preference. For example, it may be necessary Full list of author information is available at the end of the article © The Author(s) 2016. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Scalfani et al. J Cheminform (2016) 8:66 Page 2 of 8 to display the atoms as spheres, delete unwanted mol- the 3D printable crystal structure file dataset via text, ecules, or generate a unit cell. Once the desired crystal SMILES, reference, elements, and cell parameters. In structure representation is achieved, the structure is typi- addition, users can create a custom 3D printable file (STL cally exported as either a stereolithography file (STL) for or VRML) from their own CIFs and for any structure in single color 3D printing or a virtual reality modeling lan- the COD using the JSmol implementation within the 3D guage file (VRML) for multi-color printing. Lastly, files Print website. may need to be repaired of any inconsistencies in the sur- face of the 3D model (e.g. holes, overlaps) and verified for Methods compatibility with 3D printer software before printing. Programmatic processing of crystal structures into 3D In short, manual conversion of crystal structures into 3D printable files presents several challenges. One such chal- printable file formats can be a tedious and time consum- lenge is that many crystal structures contain counteri- ing process. As there are hundreds of thousands of crys- ons and solvent molecules. These companion molecules tal structures currently available in open access databases would ideally be removed from the 3D printable file for such as the Crystallography Open Database (COD) [13, two reasons: (1) most often the counterions and solvent 14], it would be ideal to automate the conversion of crys- molecules are not of direct interest for 3D printing; and tal structures (CIFs) from these databases into 3D print- (2) 3D files with multiple independent objects can be dif- able file formats. Providing quick access to 3D printable ficult for 3D printers to fabricate. While removal of coun- crystal structure files removes the barriers associated ter ions and solvent molecules can be readily achieved with file manipulation and conversion, which makes it with cheminformatics toolkits [21–23], this procedure easier for educators and researchers to 3D print crystal has not yet been applied in the preparation of small mol- structures. ecule and extended solid 3D printable crystal structure There are currently only two methods available for pro- files. grammatic conversion of a crystal structure into a 3D Another challenge with processing crystal structures printable file including the NIH 3D Print Exchange web into 3D printable files arises with the initial represen- tools developed by Coakley and coworkers at the NIH tation of the crystal structure within crystallographic [15–17] and the stand-alone Cif2VRML Windows appli- viewers. By default, many crystallographic viewing pro- cation developed by Kaminsky [18]. The NIH 3D Print grams only load the unique atom positions in the crys- Exchange web tool uses Chimera [12] and Blender [19] tallographic data, namely the asymmetric unit. This can scripts that automatically process crystal structures into lead to displaying only a fraction of a molecule or a very 3D printable files. The Cif2VRML application is writ- small segment of an extended solid. To gain a complete ten in the Delphi programming language and allows for representation of a molecule or a complete unit cell of one-click creation of 3D printable files from CIFs. The an extended solid, the software must be instructed to NIH 3D Print Exchange web tool and Cif2VRML appli- apply the appropriate space group symmetry operations cation have greatly advanced the process and efficiency to the asymmetric unit [24]. While the asymmetric unit of creating 3D printable crystal structures. However, is a useful representation, we suspect in most cases, crystal structures are still converted on an individual those interested in 3D printing crystal structures would basis; users must upload or process each crystal struc- prefer the symmetry operations applied to the crystallo- ture individually. The NIH 3D Print Exchange Team has graphic data. Applying the symmetry operations ensures made all scripting code available in the public domain, that the representation will present either one or more so researchers could adapt these scripts to program- whole molecules or a complete unit cell fragment of an matically process multiple files locally in the future [16]. extended solid. Moreover, with extended solids it is often Multiple file processing is also not currently available in useful to pack the unit cell; that is, display all atoms and the Cif2VRML application, but is being considered in a bonds that fit only within one or more unit cells. future release [18]. To overcome the aforementioned challenges of process- In this article, we report our progress to overcome the ing crystal structures into 3D printable files, we devel- current limitations with 3D printable crystal structures; oped a Jmol script, Jmol3DP (Fig. 1). When the Jmol3DP that is, the lack of programmatic multiple file conversion script is executed with a batch file from a DOS command methods. We used a Jmol [11, 20] script to program- line, the script will automatically process any number of matically