Technology Report pubs.acs.org/jchemeduc
Three Dimensional (3D) Printing: A Straightforward, User-Friendly Protocol To Convert Virtual Chemical Models to Real-Life Objects Sergio Rossi,* Maurizio Benaglia, Davide Brenna, Riccardo Porta, and Manuel Orlandi Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy S Supporting Information *
ABSTRACT: A simple procedure to convert protein data bank files (.pdb) into a stereolithography file (.stl) using VMD software (Virtual Molecular Dynamic) is reported. This tutorial allows generating, with a very simple protocol, threedimensional customized structures that can be printed by a low-cost 3D-printer, and used for teaching chemical education topics. With the use of the free licensed and multiplatform software, colored input geometries can be obtained by a simple-click modification procedure in order to generate .obj and .mtl files. An easy protocol to create personal .pdb files for 3Dprinting technology is also reported. KEYWORDS: Chemoinformatics, General Public, Hands-On Learning/Manipulatives, Molecular Modeling, Molecular Properties/Structure, Organic Chemistry
■
INTRODUCTION Hands-on experience is a fundamental component in the educational activity that greatly helps the process of science learning. The best approach to understand abstract ideal models is taking an abstract concept and bringing it to the real world, for example, building a three-dimensional object that can be easily handled. Ball-and-stick models, introduced for the first time by Hofmann in 1865,1 are often employed at the introductory level in science education to display not only the threedimensional position of the atoms in molecules but also the bonds and the dihedral angles between them. Since then, balland-stick models have found extensive application in instruction and chemistry research, and many types of models have been realized with different materials.2 Although commercial model kits are currently available, they present some problems, namely the limited variety of structures that can be represented (inorganic complexes or proteins cannot be reproduced using most molecular model kits), and their high cost. A possible solution of these limitations is the exploitation of three-dimensional (3D) printing technology, which offers the opportunity to transform scientific ideas in bespoke and low cost devices that previously required expensive and dedicated facilities to be made. In 2006, Herman3 reported a first approach for the realization of protein models through Selective Laser Sintering (SLS) 3D-printing technology. Unfortunately, the described methodology required the use of a high power laser to fuse small plastic particles, and its cost is still prohibitive for educational purposes. Scientific progress has recently made a variety of different 3D-printing technologies more accessible and more economical than SLS. The technology most often used today is known as © 2015 American Chemical Society and Division of Chemical Education, Inc.
Fused Deposition Modeling (FDM) or Fused Filament Fabrication (FFF), initially patented by S. Scott Crump4 in the late 1980s, but now supported by a large open-source development community.5 In FDM, a plastic filament is unwound from a coil, heated to a melt, and fed through a nozzle that can be moved both in horizontal and vertical direction to produce objects according to the virtual design. 3D-printers based on this technology are now accessible at low cost and are commonly available in many stores. FFF 3Dprinters have been recently employed in education programs6,7 for creating three-dimensional printed molecular models7 or proteins,8 for the visualization of potential energy surfaces,9,10 and crystals11−13 and also for the building14 of research equipment.15 Many tutorials have been reported to generate 3D-printable files from .cif (Crystallographic Information Framework) or .pdb (Protein Data Bank) files, describing how to convert chemical structures files into 3D-printed physical models.7,11 However, most of them require the use of commercial programs that have a steep learning curve. In this contribution, we provide a step-by-step description of a simple way to create .pdb files drawing structures and to convert those files in virtual files with Surface Tessellation Language (.stl) files that can be transformed by a “slicer” into gcode used by the 3D printer. We would like to point out that our procedure is neither the only nor the first method which describes how to convert a .pdb file to a “printable” file, but with respect to published procedures, it presents the following advantages: (1) a low-cost and easily accessible economical 3D printer (less than $1000) can be used;16 (2) only a free-licensed and easy-to-use software Published: July 29, 2015 1398
DOI: 10.1021/acs.jchemed.5b00168 J. Chem. Educ. 2015, 92, 1398−1401
Journal of Chemical Education
Technology Report
Figure 1. (a) 3D geometry of L-proline visualized in VDM, (b) the structure printed with a FFF 3D printer with the presence of supports, (c) the structure after the removal of supports, and (d) the colored model obtained by Sculpteo.
is employed, and (3) infinite number of structures can be generated, facilitating the retrieval of desired geometries. We used a mono extruder 3D-printer, using the same material (PLA or ABS) to print both the model and the support. It must be noted that the generated .stl file could be easily printed with a dual extruder printer also using different materials, but the printed model will be monochromatic. Colored models can be obtained by different 3D-printing technologies from FFF or by commercial 3D-printing services (such as Shapeways,16 Sculpteo,17 3dsystems18 or Ponoko19). Different input files are required for color models, but they can also be generated using the method described here.
sentation is obtained, just click on Apply and close the graphical representation tab. (3) Turn off the XYZ Axes by clicking on Display > Axes > Of f, otherwise they will be rendered into the .stl file. Remove also the Perspective visualization by selecting Display > Orthographic. (4) From the File menu, select Render. In the displayed new tab, select STL (triangle mesh only) from the “Render the current scene using” option, click on Browse to select the name (the extension .stl needs to be added) and the file destination on the PC and click on “Start rendering”. In a few seconds, the .stl file will be generated. (5) Fix eventual open surface errors using Netfabb24 free software, then load the .stl file into the 3D-printer software, adjust the printing information (such as dimensions and resolution) and print it!
■
PROCEDURE FOR GENERATING .STL FILE In this tutorial, we report a simple procedure for the conversion of a .pdb file into a .stl file using a single software package: VMD (Visual Molecular Dynamics).20 This program is a free program available for MacOS, Unix, and Windows operating systems. Furthermore, it is able to read more than 50 files with different extensions. If a given geometry cannot be found from web repositories (such as Research Collaboratory for Structural Bioinformatics21) or if it is in a format other than a .pdb file, it is possible (1) to convert it using Bable converter22 or (2) to draw it by mean of another software freeware, such as ACD/ ChemSketch23 (see Supporting Information). Assuming that the .pdb file is available, the instructions are as follows: (1) Launch VMD executable, then click on File > New Molecule. A new tab will be opened. Click on “Browse” button, and select the .pdb file. The file-path will be displayed in the Filename box and the file type will be detected automatically as PDB (this information will change if other files are selected). Click on “Load” and close the tab. The geometry of the desired molecule is displayed. (2) The desired structural representation of the molecule should be selected by click on Graphics > Representations. In this tab, the visualization of the molecule or of the protein can be adapted to personal needs. It is important to know that what we see on the screen is what will be printed out. For organic and inorganic molecules, we suggest to set the option “CPK” (Cory-Pauling-Kolton representation) in the Drawing method box to obtain the classical ball-and-stick visualization. The next step is increasing the mesh-resolution: we usually set the sphere resolution and bond resolution to 50. Many other customizations are possible. When the desired repre-
■
PROCEDURE FOR GENERATING A .OBJ AND .MTL FILE It is important to remember that .stl file specification does not contain information about colors. This is not a problem for a monoextruder FFF 3D-printer, because it can print using only one filament. FFF 3D-printers can, in principle, print with different colors, but the number of colors is limited to the number of extruders and different .stl files are required for each color. Actually, colored structures need to be printed using other technologies (more expensive than FFF) and require different input files. VMD is able to render structures in other formats than .stl; and a possible choice for 3D colored structure is to generate a wavefront .obj file containing the geometry information and a Material Library File with .mtl extension containing material definitions (such as color and texture reflection) that can be used for color 3D printing. The procedure is similar to that reported above. The only difference is point 4. In this case, in the “Render the current scene using” menu, the “Wavef ront (OBJ and MTL)” option needs to be selected. Both the files will be generated automatically during the render process. These two files can be used directly in a multicolor 3D-printer (with a different technology from FFF) or can be compressed in a .zip file and uploaded to a dedicated web portal to order the printed 3D-objects. The sequential procedure step for printing L-proline is reported in Figure 1. An example of nanotube is showed in Figure 2. 1399
DOI: 10.1021/acs.jchemed.5b00168 J. Chem. Educ. 2015, 92, 1398−1401
Journal of Chemical Education
Technology Report
be easily adapted using the 3D-printer software).26 Some examples are reported in Table 1. Particular attention must be devoted to the dimension of the printed structures. As bonds are represented as thin cylinders, it is important to set up a correct bond radius first, in order to avoid instabilities of the structure (if too thin) or esthetic problems (if too broad). In addition, the scale-up process in the printer software needs some considerations: a small object will be extremely fragile, with the possibility of breakage by handling; therefore, it is important to set the correct size of the object (and the supports) and visualize it before printing. It should be pointed out that it is possible to remove the support(s) very easily by pulling it off by hand at the end of the process.
Figure 2. (a) 3D-geometry of a nanotube visualized in VDM, (b) the structure printed with a FFF 3D-printer with the presence of supports, (c) the structure after the removal of supports.
■
CONSIDERATIONS We used the procedures reported here to generate many 3Dprintable structures, such as amino acids, sugars, nanotubes (Figure 2), proteins (Figure 3) and different cyclic structures
■
CONCLUSIONS
■
ASSOCIATED CONTENT
In conclusion, we have presented a set of simple operations to convert chemical structures in 3D-printable models. This procedure can be achieved using only free software; the userfriendly protocol is specially suitable for educational uses. This approach requires no particular programming knowledge and allows students and educators to materialize and visualize structure properties such as isomerism, conformers, reaction mechanisms, point groups and chirality. Furthermore, the realization of 3D-printed models might represent a helpful tool for blind and visually impaired (BVI) students27 to visualize and confer spatial meaning to virtual models.
S Supporting Information *
Step-by-step procedure with the use of screenshot pictures; example of chemical structures in .pdb, .stl, .obj, .mtl format. The Supporting Information is available on the ACS Publications website at DOI: 10.1021/acs.jchemed.5b00168.
■
AUTHOR INFORMATION
Corresponding Author
Figure 3. 3D-printed structure of Ubiquitin protein after supports removal.
*E-mail:
[email protected]. Notes
conformations. A detailed list of structures is reported in the Supporting Information. The approximate cost for a printed model is determined by the material-type used during the printing process. We use PLA polymer filament, and the price25 range of a model is $1−5 depending on the final size (generally all models were printed with 10 cm length, but dimension can
The authors declare no competing financial interest.
■
ACKNOWLEDGMENTS S.R. thanks Università degli Studi di Milano for a postdoctoral fellowship.
Table 1. Selected Molecules and Characteristics for 3D-Printing Structurea Cyclohexane (boat conformation) Cyclohexane (chain conformation) L-proline PCl3 H2SO4 Ubiquitin (1UBQ) protein Nanotube
Dimension (mm3) 90 90 92 60 70 80 79
× × × × × × ×
88 × 63 73 × 61 64 × 52 49 × 39 71 × 80 118 × 97 80 × 120
Filament (g)b
Cost ($)
60 41 27 13 33 60 86
2.04 1.39 0.92 0.44 1.12 2.04 2.92
All these structures were successfully printed using a Sharebot NG 3D printer. bAmount could vary depending on filling. We generally set a 50% fill for objects and 30% fill for supports. a
1400
DOI: 10.1021/acs.jchemed.5b00168 J. Chem. Educ. 2015, 92, 1398−1401
Journal of Chemical Education
■
Technology Report
(17) “Sculpteo | Online 3D Printing Service for your 3D design” http://www.sculpteo.com/en/ (accessed Jun 2015). (18) “Quickparts | www.3dsystems.com” http://www.3dsystems. com/quickparts (accessed Jun 2015). (19) “Ponoko” https://www.ponoko.com/(accessed Jun 2015). (20) “VMD - Visual Molecular Dynamics” http://www.ks.uiuc.edu/ Research/vmd/ (accessed Jun 2015). (21) “RCSB Protein Data Bank - RCSB PDB” http://www.rcsb.org/ pdb/home/home.do (accessed Jun 2015). (22) O’Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeersch, T.; Hutchison, G. R. Open Babel: An open chemical toolbox. J. Cheminf. 2011, 3, 33. (23) “ACD/ChemSketch for Academic and Personal Use:: ACD/ Labs.com” http://www.acdlabs.com/resources/freeware/chemsketch/ (accessed Jun 2015). (24) “netfabb Software - Software for 3D Printing - 3D Software for STL files - fixing, repair, editing, merge STL data for Rapid Manufacturing - STL Viewers and STL repair” http://www.netfabb. com/(accessed Jun 2015). (25) Sharebot official Web site reported 24.50 € for 0.750 kg of PLA. However, price may vary depending on the supplier. (26) We use a single extruder Sharebot NG 3D printer, with a printed area of 250 × 200 × 200 mm3 (±5 mm). (27) Wedler, H. B.; Cohen, S. R.; Davis, R. L.; Harrison, J. G.; Siebert, M. R.; Willenbring, D.; Hamann, C. S.; Shaw, J. T.; Tantillo, D. J. Applied Computational Chemistry for the Blind and Visually Impaired. J. Chem. Educ. 2012, 89, 1400−1404.
REFERENCES
(1) Ball-and-stick model was displayed on 7 April 1865, during the Friday Evening discourse at the Royal Institution: “On the Combining Power of Atoms”, Proc. R. Inst. G. B. 1865, 4, No. 42, 416. (2) (a) Mann, A. W. Models for simple, close-packed crystal structures. J. Chem. Educ. 1973, 50, 652−653. (b) Bindel, T. H. Crystal Models Made from Clear Plastic Boxes and Their Use in Determining Avogadro’s Number. J. Chem. Educ. 2002, 79, 468−472. (c) Kenney, M. E. Permanent packing type crystal models. J. Chem. Educ. 1958, 35, 513−513. (d) Gibb, T. R. P.; Bassow, H. Construction of crystal models from styrofoam spheres. J. Chem. Educ. 1957, 34, 99−101. (e) Birk, J. P.; Foster, J. Molecular models for the do-it-yourselfer. J. Chem. Educ. 1989, 66, 1015−1018. (f) Siodłak, D. Building Molecular Models Using screw-On Bottle Caps. J. Chem. Educ. 2013, 90, 1247− 1249. (g) Scattergood, A. The making of crystal lattice and unit cell models. J. Chem. Educ. 1937, 14, 140−140. (h) He, F.; Liu, L.; Li, X. Molecular models constructed in an easy way. Part 1. Models of tetrahedron, trigonal bipyramid, octahedron, pentagonal bipyramid, and capped octahedron. J. Chem. Educ. 1990, 67, 556−558. (i) He, F.; Lubin, L.; Li, X. Molecular models constructed in an easy way. Part 2. Models constructed by using tetrahedral units as building blocks. J. Chem. Educ. 1990, 67, 650−652. (l) Chuang, C.; Jin, B.; Tsoo, C.; Tang, N. Y. W.; Cheung, P. S. M.; Cuccia, L. A. Molecular Modeling of Fullerenes with Beads. J. Chem. Educ. 2012, 89, 414−416. (3) Herman, T.; Morris, J.; Colton, S.; Batiza, A.; Patrick, M.; Franzen, M.; Goodsell, D. S. Biochem. Mol. Biol. Educ. 2006, 34, 247− 254. (4) Crump, S. S. Apparatus and methods for creating threedimensional object Patent US5121329 June 9, 1992. (5) See (a) reprap.org (accessed Feb 2015) and (b) Wittbrodt, B. T.; Glover, A. G.; Laureto, J.; Anzalone, G. C.; Oppliger, D.; Irwin, J. L.; Pearce, J. M. Life-cycle economic analysis of distributed manufacturing with open-source 3D printers. Mechatronics 2013, 23, 713−726. (6) Flint, E. B. Teaching Point-Group Symmetry with ThreeDimensional Models. J. Chem. Educ. 2011, 88, 907−909. (7) Scalfani, V. F.; Vaid, T. P. 3D Printed Molecules and Extended Solid Models for Teaching Symmetry and Point Groups. J. Chem. Educ. 2014, 91, 1174−1180. (8) Chakraborty, P.; Zuckermann, R. N. Coarse-grained, foldable, physical model of the polypeptide chain. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 13368−13373. (9) Blauch, D. N.; Carroll, F. A. 3D Printers Can Provide an Added Dimension for Teaching Structure−Energy Relationships. J. Chem. Educ. 2014, 91, 1254−1256. (10) Teplukhin, A.; Babikov, D. Visualization of Potential Energy Function Using an Isoenergy Approach and 3D Prototyping. J. Chem. Educ. 2015, 92, 305−309. (11) Chen, T.-H.; Lee, S.; Flood, A. H.; Miljanić, O. Š. How to print a crystal structure model in 3D. CrystEngComm 2014, 16, 5488−5493. (12) Kaminsky, W.; Snyder, T.; Stone-Sundberg, J.; Moeck, P. Oneclick preparation of 3D print files (*.stl, *.wrl) from *.cif (crystallographic information framework) data using Cif2VRML. Powder Diffr. 2014, 29, S42. (13) Kitson, P. J.; Macdonell, A.; Tsuda, S.; Zang, H. Y.; Long, D. L.; Cronin, L. Bringing Crystal Structures to Reality by Three-Dimensional Printing. Cryst. Growth Des. 2014, 14, 2720−2724. (14) (A) Pearce, J. M. Materials science. Building research equipment with free, open-source hardware. Science 2012, 337, 1303−1304. (b) Pearce, J. M. Open-Source Lab: How to Build Your Own Hardware and Reduce Research Costs; Elsevier: Boston, MA, 2014. (15) Files for printing these objects are often shared on free and open repository such as Thingiverse. See www.thingiverse.com (accessed Feb 2015). There are many examples of vial racks, Buchner funnels, microtiter plates, customizable filter wheel, filter bracket, holders, lab jack and so on [thing:25080, thing:25188, thing:11621, thing:26553] and also ref 14b. (16) “Shapeways - 3D Printing Service and Marketplace” https:// www.shapeways.com/ (accessed Jun 2015). 1401
DOI: 10.1021/acs.jchemed.5b00168 J. Chem. Educ. 2015, 92, 1398−1401
