Putting 3D-print files of crystallographic models into open access

1. Putting 3D-print files of crystallographic models into open access International Advisory Board of the Crystallography Open Database & T. J. Snyder trevor.snyder@3dsystems.com Modern crystallography has come a long way over the past 100 years; from a model of the very first crystal structure ever elucidated [1], Fig. 1, all the way to permanent URIs (on the Internet) for the structures of more than 250,000 small molecules and small to medium sized unit cell materials [2-4], Fig. 2. With the Crystallographic Information Framework (CIF,*.cif), there is a generally accepted and well documented “computer readable language of crystallography” [5]. Low cost 3D printing which utilizes the STereoLithography (STL,*.stl) format of 3D Systems Corporation became available recently, Fig. 3. It meets (and exceeds) the quality and low-cost maintenance needs of crystallographers (and the general public) for less than $1,000 [6]. Reduced cost and increased performance trends are expected to continue within the next few years, Fig. 4. Realizing that crystallographers now need conversion programs from CIF to STL to make good use of these recent developments, Werner Kaminsky incorporated such a converter into his well known WinXMorph program and created the CIF2VRML program from scratch [7]. While CIF2VRML reads small and macro-molecule *.cif files, displays them in the standard virtual reality format (VRML) and allows for exports into *.stl files, WinXMorph does the same (and much more) for crystal morphologies. Figure 5 shows an annotated flow chart for the 3D printing of a model of a sugar molecule (of the kind that some of you may like to put into your coffee, i.e. sucrose). A partial flow chart for the 3D printing of a sucrose crystal complements this figure. Fig. 2 Promotional coffee mug from the International Advisory Board of the COD with the permanent URI of the caffeine molecule. We put crystallographic data into the public domain; it is up to you to use them and also to upload your own data to our website [2]. Fig. 1 Hard sphere model of the diamond structure by W. H. Bragg, Museum of the Royal Institution, London, photographed by Prof. André Authier. Taken from: http://blog.oup.com/2013/08/100th-anniversary-first-crystal-structure-determinations-bragg/#sthash.50BE8wiT.6mYKaBKB.dpuf and properly acknowledged below. Fig. 3 An inexpensivemulti-color 3D printer from 3DSYSTEMS (less than $1,000), ref. [6], on the basis of their Plastic Jet 3D printing technology. Fig. 4 Mid 2012 “expectations versus time”graph of the Gartner group, showing 3D printing at the “peak of inflated expectations” and extrapolating to its “plateau of productivity” in 2017 (to 2022 at the latest). We are committed to put all produced *.stl files into open access over time, beginning at a COD related project site that focuses on education [8]. Crystallography Open Database solid sugar_for_your_coffee STL facet normal -0.13 -0.13 -0.98 outer loop vertex -16.25 14.23 -5.82 vertex -16.25 12.06 -5.54 vertex -18.42 14.23 -5.54 endloop endfacet facet normal 0.13 0.13 -0.98 outer loop vertex -16.25 14.23 -5.82 vertex -16.25 16.40 -5.54 vertex -14.08 14.23 -5.54 endloop endfacet… endsolid sugar_for_your_coffee STL data_sugar_for_your_coffee _chemical_formula_sum 'C12 H22 O11' loop_ _atom_site_type_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z C 0.1310(2) 0.3413(3) 0.87541(17) C 0.2853(2) 0.3437(3) 0.99294(17) H 0.2730 0.4343 1.0421 C 0.4450(2) 0.3665(3) 0.93456(17) H 0.4824 0.2702 0.9045 C 0.3720(2) 0.4730(3) 0.82356(19) H 0.3889 0.5780 0.8527 C -0.0439(2) 0.4042(3) 0.89730(19) H -0.0222 0.4998 0.9419 H -0.1256 0.4222 0.8166 C 0.4528(2) 0.4517(3) 0.7107(2) H 0.3838 0.5085 0.6399 H 0.5717 0.4931 0.7306 C 0.2044(2) -0.0172(3) 0.64090(19) H 0.2815 -0.0248 0.7258 C 0.0583(2) -0.1374(3) 0.6261(2) H -0.0112 -0.1367 0.5386 C -0.0643(2) -0.1014(3) 0.71470(19) H 0.0024 -0.1084 0.8028 C -0.1356(2) 0.0589(3) 0.68727(18) H -0.2070 0.0621 0.6003 C 0.0147(2) 0.1767(3) 0.70012(17) H -0.0375 0.2754 0.6725 C 0.3159(2) -0.0370(3) 0.54289(19) H 0.4141 0.0335 0.5609 H 0.3642 -0.1386 0.5490 O 0.18374(14) 0.4395(2) 0.78776(13) O 0.10890(15) 0.18775(17) 0.82869(12) O 0.13181(16) 0.13534(19) 0.62240(13) O -0.12087(17) 0.2987(2) 0.97007(14) H -0.1435 0.2194 0.9306 O 0.29571(17) 0.2162(2) 1.07411(13) H 0.3169 0.1401 1.0370 O 0.58915(15) 0.4375(2) 1.02170(14) H 0.6818 0.3941 1.0197 O 0.46070(18) 0.2959(2) 0.67330(16) H 0.3607 0.2599 0.6566 O -0.24737(17) 0.0983(2) 0.77112(14) H -0.3239 0.1577 0.7355 O -0.2031(2) -0.2133(3) 0.69108(16) H -0.2344 -0.2307 0.7567 O 0.1446(2) -0.2792(2) 0.6518(2) H 0.0703 -0.3464 0.6462 O 0.2142(2) -0.0121(3) 0.41865(14) H 0.2172 0.0779 0.4012 … _space_group.point_group_H-M '2' loop_ _exptl_crystal_face_index_h _exptl_crystal_face_index_k _exptl_crystal_face_index_l _exptl_crystal_face_perp_dist -1 -1 0 0.51 -1 -1 1 0.584 -1 0 0 0.5681 … http://www.crystallography.net 3D printing, approx. $50 currently, 1/10 of that in the near future Werner’s downloadable software [7] (donations welcomed – otherwise free) CIFs from open access databases, e.g. the COD(both figures to the right from ref. [4]) or its little “educational offsprings” (below, ref. [8]) [8a] ~ $5 currently, 1/10 of that in the near future [8b] just kidding ? Sure, you have much better uses for these kinds of models ! more 3D print files downloadable in the future ? Fig. 5 Annotated flow charts for the 3D printing of models of a sucrose molecule (complete) and crystal (partial). [1] W. H. Bragg and W. L. Bragg, The structure of diamond, Proc. R. Soc. Lond. A 89, 277 (1913) [2] www.crystallography.net; http://cod.ibt.lt/, http://cod.ensicaen.fr/, http://qiserver.ugr.es/cod/, http://nanocrystallography.org , and http://nanocrystallography.research.pdx.edu [3] S. Gražulis, D. Chateigner, R. T. Downs, A. F. T. Yokochi, M. Quirós, L. Lutterotti, E. Manakova, J. Butkus, P. Moeck, and A. Le Bail, Crystallography Open Database – an open-access collection of crystal structures, J. Appl. Cryst.42, 726 (2009); http://journals.iucr.org/j/issues/2009/04/00/kk5039/kk5039.pdf, grazulis@ibt.lt [4] S. Gražulis, A. Daškevič, A. Merkys, D. Chateigner, L. Lutterotti, M. Quirós, N. R. Serebryanaya, P. Moeck, R. T. Downs, and A. Le Bail, Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration, Nucleic Acids Research40,D420 (2012); http://nar.oxfordjournals.org/content/40/D1/D420.full.pdf+html, grazulis@ibt.lt [5] S. R. Hall, F. H. Allen, and I. D. Brown, The Crystallographic Information File (CIF): A New Standard Archive File for Crystallography, Acta Cryst. A 47, 655 (1991); http://www.iucr.org/iucr-top/cif/standard/cifstd1.html and http://www.iucr.org/resources/cif for continued updates as this standard progresses [6] January 6, 2014, press release:http://www.3dsystems.com/press-releases/3d-systems-recasts-consumer-3d-printing-experience-new-cuber-3 ; promotion: http://www.youtube.com/watch?feature=player_embedded&v=Osu5MC2PtMI; http://www.3dsystems.com/press-releases/3d-systems-ups-prosumer-standards-new-sub-5000-cubeprotm-3d-printer ; http://www.3dsystems.com/press-releases/3d-systems-launches-cubifyr-20 [7]Prof. Werner Kaminsky: http://cad4.cpac.washington.edu/; CIF2VRML: http://cad4.cpac.washington.edu/cif2vrmlhome/cif2vrml.htm; WinXMorph: http://cad4.cpac.washington.edu/WinXMorphHome/WinXMorph.htm, kaminsky@chem.washington.edu [8] http://nanocrystallography.research.pdx.edu/search/edu/, pmoeck@pdx.edu; [8a] http://nanocrystallography.research.pdx.edu/media/sugar_molecule_stl.stl ; [8b] http://nanocrystallography.research.pdx.edu/media/sugar_morphology_stl.stl Support from NSF grant EEC-1242197 is gratefully acknowledged. Prof. André Authier is thanked for Fig. 1 which we took from his blog:http://blog.oup.com/2013/08/100th-anniversary-first-crystal-structure-determinations-bragg/#sthash.50BE8wiT.6mYKaBKB.dpuf. No kidding, this work is one of our personal contributions to theUNESCO International Year of Crystallography (2014).