Transcript Fig. 1 - Open Access Crystallography

Putting 3D-print files of crystallographic models
into open access
[email protected]
International Advisory Board of the Crystallography Open Database & T. J. Snyder
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.
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-crystalstructure-determinations-bragg/#sthash.50BE8wiT.6mYKaBKB.dpuf and
properly acknowledged below.
Fig. 3 An inexpensive
multi-color 3D printer
from 3DSYSTEMS (less
than $1,000), ref. [6], on
the basis of their Plastic Jet
3D printing technology.
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.
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).
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.
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
data_sugar_for_your_coffee
solid sugar_for_your_coffee STL
_chemical_formula_sum
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
'C12 H22 O11'
http://www.crystallography.net
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]
[8b]
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'
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).
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
…
Werner’s downloadable software [7]
(donations welcomed – otherwise free)
~ $5 currently, 1/10 of
that in the near future
Sure, you have much
better uses for these
kinds of models !
[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, [email protected]
[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 Research 40, D420 (2012); http://nar.oxfordjournals.org/content/40/D1/D420.full.pdf+html, [email protected]
[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,
[email protected]
[8] http://nanocrystallography.research.pdx.edu/search/edu/, [email protected]; [8a] http://nanocrystallography.research.pdx.edu/media/sugar_molecule_stl.stl ; [8b] http://nanocrystallography.research.pdx.edu/media/sugar_morphology_stl.stl
3D printing, approx. $50
currently, 1/10 of that in
the near future
just kidding
?
?
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/2013/08/100thanniversary-first-crystal-structure-determinationsbragg/#sthash.50BE8wiT.6mYKaBKB.dpuf.
No kidding, this work is one of
our personal contributions to
the UNESCO International Year
of Crystallography (2014).