Volume 16 Number 25 7 July 2014 Pages 54775742

CrystEngComm
www.rsc.org/crystengcomm

HIGHLIGHT
Teng-Hao Chen et al.
How to print a crystal structure model in 3D

Open Access Article. Published on 04 April 2014. Downloaded on 26/03/2015 00:35:55.

This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence.

CrystEngComm
View Article Online

HIGHLIGHT

View Journal | View Issue

How to print a crystal structure model in 3D

Cite this: CrystEngComm, 2014, 16,
5488

Teng-Hao Chen,*a Semin Lee,b Amar H. Floodb and Ognjen . Miljania

We present a simple procedure for the conversion of Crystallographic Information Files (CIFs) into Virtual

Received 19th February 2014,

Accepted 4th April 2014
DOI: 10.1039/c4ce00371c
www.rsc.org/crystengcomm

Reality Modelling Language (VRML2, .wrl) files, which can be used as input files for three-dimensional
(3D) printing. This procedure permits facile production of customized full-colour 3D models of X-ray
crystal structures of segments of extended structures, including metalorganic frameworks (MOFs) as
well as small molecules. The method uses freely available software that runs under Microsoft Windows,
MacOSX and Linux operating systems.

Introduction
Three-dimensional (3D) printing or additive manufacturing is
a process of making a three-dimensional solid object of virtually any shape from a digital model. This powerful technology
is no longer futuristic, as the cost of 3D printing has dropped
dramatically over that past decade, making it affordable even
to a hobbyist. 3D printing has been touted as ushering the
third industrial revolutionthat of mass customization,
wherein virtually any consumer object could be tailored to a
previously unprecedented level.1 This technology will likely
a

Department of Chemistry, University of Houston, 112 Fleming Building, Houston,

Texas 77204-5003, USA. E-mail: tchen21@uh.edu; Fax: +1 713 743 2709; Tel: +1
832 842 8827
b
Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue,
Bloomington, Indiana 47405, USA+1 812 856 3642
Electronic supplementary information (ESI) available: (a) Source files (.cif,
.pdb, .x3d, .wrl) for all stages of production of the MOFF-3 3D structure model;
(b) an addendum on 3D printing of dynamic models of supramolecular complexes and mechanically interlocked molecules; and (c) movies of those complexes/molecules in motion. See DOI: 10.1039/c4ce00371c

Teng-Hao Chen

Teng-Hao Chen received a

BS degree in Chemistry from
National Taiwan University in
2006. After graduation, he worked
as a research assistant in the
Industrial Technology Research
Institute in Hsinchu, Taiwan for
one year. He is currently
pursuing a PhD in Chemistry at
the University of Houston in
Prof. Ognjen Miljani's group.
His research focuses on the
synthesis and applications of
novel porous materials.

5488 | CrystEngComm, 2014, 16, 54885493

revolutionize numerous fields of human activity; as just one

example, prosthetic medicine could soon count on implants
perfectly matching each individual patient. 3D printing is
beginning to affect chemical research as well: Cronin et al.
have recently reported the creation of customized 3D-printed
reactionware, the composition and shape of which allow its
active participation in the reaction and analysis of products.2
Chemistry is full of concepts that require three-dimensional
understanding, and representing those in two-dimensional
PowerPoint slides, journal articles, or on chalkboards inevitably leads to a loss of detail. Crystallography is even more
dependent on 3D representations, and most readers of this
journal have likely spent numerous hours turning crystal
structure models on their computer screens to produce a view
that sacrifices the least information. An ability to easily build
3D models of crystal structures is thus clearly needed. In this
contribution, we provide step-by-step instructions on how to
convert a .cif filewhich is a typical end product of crystal
structure refinementinto a 3D-printed physical model of a
crystal structure. We use MOFF-3 (Fig. 1)one of our previously published extended metalorganic framework (MOF)

Semin Lee received his BS (2006)

and MS (2008) degrees at
Sogang University, South Korea,
under the supervision of Bongjin
Moon. In fall 2009, he joined
Professor Amar Flood's laboratory at Indiana University as a
PhD student. His research is
focused on designing new anion
receptor molecules, such as
cyanostars, and investigating
their materials properties.
Semin Lee

This journal is The Royal Society of Chemistry 2014

View Article Online

Open Access Article. Published on 04 April 2014. Downloaded on 26/03/2015 00:35:55.

This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence.

CrystEngComm

Fig. 1 The starting point: 2D representation of the MOFF-3 structure

produced directly from its .cif file using Mercury 3.3.

structures3as an illustration for this method. This procedure

is broadly applicable to many other structures; in our two labs,
we have printed 3D models of more than thirty different small
molecules and MOFs.
Our procedure is neither the only nor the first method for
achieving the conversion of crystallographic information
files into 3D printed models.4 Its advantages are: (a) the ability
to produce models of both discrete molecules and segments of extended infinite structures such as MOFs; (b) the
use of freely available and highly intuitive software packages
(vide infra) with ample helpful documentation available online;
and (c) its reliance on a commercial 3D printing service provided by Shapeways, which obviates the need for an in-house
3D printer.
The main disconnect between the crystal structure manipulation programs and the 3D printing software lies in the mutual
incompatibility of file formats. Out of the commonly used
crystal structure processing programs, only PyMOL5 is able to
directly export crystal structure data contained in .cif files into
the VRML (.wrl) format most commonly used for colour 3D

Amar H. Flood was born in

New Zealand where he received
his BSc (Hons) and PhD (2001)
from Otago University with
Keith C Gordon. During his
postdoctoral studies at UCLA
with Fraser Stoddart, his appreciation for visual representations of chemistry grew. In 2005,
he started as an Assistant
Professor at Indiana University
and in 2009 printed his first
molecular models in 3D. He is a
Amar H. Flood
Camille Dreyfus Teacher-Scholar
and the James F. Jackson Associate Professor of Chemistry. He is
the recipient of a NSF CAREER Award, Cram Lehn Pedersen Prize
and the Award for Early Excellence in Physical Organic Chemistry.
His research interests are anion recognition, molecular switches
and surface self-assembly.

This journal is The Royal Society of Chemistry 2014

Highlight

printing.6 This feature enables the printing of small molecule

models via PyMOL (see the ESI for photos and movies of 3D
models of selected small molecules: triazolophanes,7
cyanostars8 and cyanostar-[3]rotaxane). However, many crystal
structure processing operationse.g. connectivity expansion,
addition of multiple unit cells, etc.are rather difficult to do in
PyMOL. Our protocol thus resorts to using two programs
which together offer greater flexibility in manipulating both
the crystal structure and the 3D model. Mercury9 is used to produce a .pdb file of the crystal structure, which is then imported
into Blender10a semi-professional 3D printing programfor
additional processing and conversion into a .wrl file. This
combination is necessary since Blender appears to be unable to
import .pdb files produced by programs other than Mercury.

Procedure
Four separate pieces of software are required for this conversion: Mercury 3.3,9 Blender 2.62 and 2.69,10 and the opensource embedded Python Molecular Viewer (ePMV) plugin,
which runs molecular-modelling software directly in
Blender.11 In our work, we used the Windows versions of
these programs as well as MacOSX (Mercury 3.1.1 and
Blender 2.62 and 2.70); since all of the requisite programs
are also available for the Linux operating system, it is reasonable to assume that a very analogous procedure should function on this platform as well.
Instructions are as follows:
1. Set user preferences in Blender 2.62. Open Blender 2.62
then click on File > User Preferences > Addons. Make sure
that under the Importexport tab, option Web3D X3D/VRML
format is checked. Under the System tab, options autoPack,
ePMV and ePMV synchro should all be checked. Click on
Save as Default. As a result, ePMV and autoPACK buttons

Ognjen . Miljani was born in

Belgrade, then Yugoslavia, in
1978. He holds a Diploma
(2000) from the University of Belgrade and a PhD (2005, with
Peter Vollhardt) from UC Berkeley. In 2008, following a postdoctoral stay at UCLA with Fraser
Stoddart, Ognjen started his
independent career as an Assistant Professor at the University
of Houston. He is the recipient
of the 2012 NSF CAREER and
Ognjen . Miljani
2013 Cottrell Scholar awards.
His research interests include dynamic combinatorial libraries
and metalorganic frameworks.

CrystEngComm, 2014, 16, 54885493 | 5489

View Article Online

Open Access Article. Published on 04 April 2014. Downloaded on 26/03/2015 00:35:55.

This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence.

Highlight

will show in the upper right corner of the Blender 2.62

window.
2. Set user preferences in Blender 2.69. Open Blender 2.69
then click on File > User Preferences > Addons. Make sure
that under the Importexport tab, options Web3D X3D/VRML
format and VRML2 (Virtual Reality Modelling Language) are
both checked. Under the Mesh tab, option 3D Print Toolbox
should be checked. Click on Save User Settings.
3. Open the crystal structure's CIF file in Mercury and
produce the desired packing (one or more molecules/unit
cells). At this stage, it may be also useful if disordered atoms
or side chains are deleted so that only one orientation
remainsunless the objective is to highlight the disorder.
To delete undesired features of the structure, click on
Edit > Edit Structure > Remove, and then click on the
atoms or molecules that need to be removed.
4. The resulting data should be saved as a PDB file (File >
Save As). In our case, only PDB files produced by Mercury
could be successfully used in the subsequent steps.
5. Open Blender 2.62 and click on the ePMV button on the
top right. As a result, the ePMV interface will appear on the leftside panel. Delete the cube, camera, and light objects in the
main Blender window (this is done by simply right-clicking on
those objects followed by pressing the Delete button).
6. In the ePMV panel, choose Browse and navigate to the
PDB file produced in step 4. Upon loading, a series of dots
will appear in the main Blender window; these represent
individual atoms.
7. In the Atom/Bond Representation subpanel on the left,
choose the desired structural representation; for most organic
and inorganic structures, Atoms or Sticks representations are
the most appropriate. The ensuing calculation will take
between several seconds and several hours depending on the
complexity of the structure. Values for the cpk_scale, bs_scale,
and bs_ratio, as well as element colours should be adjusted at
this point (if desired), since further changes are not permitted
after the file is saved. Changing these parameters will affect
all atoms (or bonds) of a given kind; individual atoms can
also be modified using the description given in step 10 below.
8. Save the file and export it as an .x3d file: click on File >
Export > X3D Extensible 3D (.x3d).
9. Close Blender 2.62 and open Blender 2.69. Import the
.x3d file created in the previous step: click on File > Import
> X3D Extensible 3D (.x3d).
10. In Object Mode, you can select and delete individual
atoms and bonds and adjust the size of any item (Fig. 2, top).
For example, to adjust the size of an atom, right-click on
the desired atom and choose Scale in the Object Tools on
the interface on the right. To change the color of atoms
and bonds, click on the Material icon . Click () to remove
the original material and (+) to add a new one. The color
can be adjusted using the Diffuse option. You can rename
the material and click
to save it then apply it to any
item that you want to have the same color. This feature is
particularly useful if certain parts of the structure need to
be emphasized.

5490 | CrystEngComm, 2014, 16, 54885493

CrystEngComm

11. The produced model will most likely need to be

resized to be of dimensions that are practical for printing.
To do so, click on the Scene button on the right-side panel
(third button from the left; highlighted in red in Fig. 2,
bottom). Change Units to Metric. Then, select all atoms by
pressing A (with the cursor located in the view window),
which should result in the entire structure being highlighted
in the main Blender window. Click on Join on the left-side
panel to connect all of the separate parts, and then use the
Scale button in the left-side panel to adjust the size of the
structure. We have typically found the originally imported
structures to be too large, and most of them needed to be
scaled down. It should be noted that the dimensions provided by Blender do not correlate well with the size of the
printed model (vide infra), so adjustment of dimensions for
3D printing requires some trial and error.
12. Once satisfied with the model size, click on the Object
Mode button on the bottom left and switch the selection to
Edit Mode. Then, press W (with the cursor located in the view
window) and click on Remove Doubles, which should remove
artefact vertices in the structure.
13. Export the resultant data to a VRML2 (.wrl) file: click
on File > Export > VRML2 (.wrl).
14. The created .wrl file can now be handled by many
commercial and academic 3D-printing facilities. Models
presented in this work have been printed by the popular
website Shapeways.12 After brief user registration, the source
file can be uploaded onto the Shapeways website by clicking
on Make + Sell > Upload > Select 3D File and then choosing
the produced .wrl file. Units should be set to inches, and the
Upload Now button should be clicked. The Shapeways website
will then perform the upload, estimate the model size, and
confirm whether the model is indeed printable. The two most
commonly encountered problems during the upload are the
large file sizes (Shapeways imposes a limit of 64 megabytes,
which can be somewhat expanded by uploading compressed
ZIP files) and a large number of polygons. The latter are
created during conversion of the structure in Blender and
their number can be checked by consulting the Tris number
on the top-right bar in the Blender window (Fig. 2, bottom).
Shapeways limits the complexity of the uploaded models to
1 000 000 polygons.
15. If the model size is not satisfactory, the model should
be scaled again (steps 11 and onward) and the process
repeated until a desired size is obtained as the estimate.
Once the model size is finalized, the Shapeways team will
check the printability of the proposed model and inform the
user if there are potential issues. If no error is reported, the
model can be printed. All that remains is to choose a material for the 3D model. At the time of this writing, Shapeways
offered a wide variety of plastic, ceramic and metallic substrates
(steel, silver, brass, bronze), but the only material offering
full-colour functionality was Full Color Sandstone, a proprietary mixture of plasters, vinyl polymers, and carbohydates.13
Incidentally, this is one of the least expensive 3D printing
materials offered. If a monochromatic model is desired,

This journal is The Royal Society of Chemistry 2014

View Article Online

Highlight

Open Access Article. Published on 04 April 2014. Downloaded on 26/03/2015 00:35:55.

This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence.

CrystEngComm

Fig. 2 Exemplary screenshots during the processing of crystal structure data using Blender. Specific buttons required in this procedure are
highlighted in red; refer to the text for details.

we anticipate that most other materials would function well

(although we have not tested them).
16. If printability errors are reported, they are most commonly related to the physical limitations of the sandstone
material used in printing. Thus, structures with many bonds
may make those bonds too thin (<2 mm) to support themselves;
in such cases, either a smaller fragment of the structure should

This journal is The Royal Society of Chemistry 2014

be chosen for printing or the representation should be switched

to Space-filling, with larger cpk_scale values used in step 7.
An example of a finished model is shown in Fig. 3. At current
(February 2014) prices, a model similar to the one shown in
Fig. 3 will cost between $20 and $100 depending on the size.14
Because sandstone is essentially plaster, models produced
from it are rather fragile (they will easily shatter if dropped),

CrystEngComm, 2014, 16, 54885493 | 5491

View Article Online

Highlight

CrystEngComm

Open Access Article. Published on 04 April 2014. Downloaded on 26/03/2015 00:35:55.

This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence.

Acknowledgements

Fig. 3 The finished product: 3D printed model of the MOFF-3 structure.

Approximate dimensions: 16 8 7 cm.

thermostable only up to 60 C, not resistant to water and

have grainy surfaces. There are two solutions to the last two
problems. First, the printed model can be dipped in glue
(e.g. ZPrinter Z-Bond 90 Infiltrant) to form a coating that
gives a strengthened material with a glossy finish when dried.
The usage and safety instructions for this product should be
followed. For example, when the models are dipped into a
plastic container full of the glue, there is a large temperature
increase (exothermic) and outgassing is significant enough to
warrant the use of personal protective equipment and a ventilated area (fume hood). The model is then patted dry to remove
excess glue. The glue penetrates ~2 mm into the model; excess
glue will pool and deteriorate the finish. A simpler method
that gives similar results makes use of a glossy acrylic spray
that can be applied with repetitive spraydry cycles (45 times).

Conclusions
In conclusion, we presented here a set of guidelines on how
to convert any small-molecule or extended material crystal
structure into a 3D printed model. The value of these models
should be in facilitating communication of crystal structure
details both in the classroom and between experienced practitioners in the field. Our set of instructions uses freely available software, requires no programming knowledge and no
knowledge of 3D printing techniques, and produces models
using a commercial easy-to-use website.
As with many rapidly developing technologies, we expect
these instructions to be outdated within several years, as
3D printers enter the mainstream and crystal structure processing software becomes better integrated with this
obviously very relevant technology. Until then, we hope that
our colleagues will find this protocoland its 3D-printed
productsuseful and educational.

Note added in proof

During the production of this paper, two related papers also in
production came to our attention: (a) P. Kitson, A. Macdonell,
S. Tsuda, H. Zang, D.-L. Long and L. Cronin, Cryst. Growth Des.,
2014, 10.1021/cg5003012. (b) V. F. Scalfani and T. P. Vaid,
J. Chem. Educ., 2014, 10.1021/ed400887t.

5492 | CrystEngComm, 2014, 16, 54885493

This work was supported by the National Science Foundation

CAREER program (awards CHE-1151292 to O. . M., CHE-0844441
to A. H. F.), the Welch Foundation (award E-1768 to O. . M.)
and the donors of the American Chemical Society Petroleum
Research Fund (award DNI-50390 to O. . M.). O. . M. is a
Cottrell Scholar of the Research Corporation for Science
Advancement. A. H. F. is a Camille Dreyfus Teacher-Scholar
and S. L. is a Chester Davis Fellow. S. L. and A. H. F. thank
Nicole Jacquard, the Department of Fine Arts, and the
Advanced Visualization Lab at Indiana University for printing.

Notes and references

1 Additive Manufacturing: Solid Print, in The Economist
Special Report on Manufacturing and Innovation, April 21
2012, pp. 1415.
2 (a) J. S. Mathieson, M. H. Rosnes, V. Sans, P. J. Kitson and
L. Cronin, Beilstein J. Nanotechnol., 2013, 4, 285291; (b)
P. J. Kitson, M. D. Symes, V. Dragone and L. Cronin, Chem.
Sci., 2013, 4, 30993103; (c) P. Kitson, M. Rosnes, V. Sans,
V. Dragone and L. Cronin, Lab Chip, 2012, 12, 32673271;
(d) M. D. Symes, P. J. Kitson, J. Yan, C. J. Richmond,
G. J. T. Cooper, R. W. Bowman, T. Vilbrandt and L. Cronin,
Nat. Chem., 2012, 4, 349354.
3 T.-H. Chen, I. Popov, O. Zenasni, O. Daugulis and
O. . Miljani, Chem. Commun., 2013, 49, 68466848.
4 For examples of printing structures of distinct proteins, see:
http://cbe.wisc.edu/assets/docs/pdf/srp-bio/stongrevised.pdf.
For small molecules and proteins, see: http://barneybioproductslab.
cfans.umn.edu/3d-printing-and-molecular-models/. For a
commercial service offering 3D printed molecular models,
see: http://models.scripps.edu/. See also: N. Jones, Nature,
2012, 487, 2223.
5 The PyMOL Molecular Graphics System, Version 1.5.0.4,
Schrdinger, LLC. Freely available from: www.pymol.org.
6 It should be noted that other 3D printing file formats (e.g. .STL)
can be used if colour models are not required. There is
much instructional value in monochromatic models as well,
since they can be printed quickly and inexpensively on many
of the hobbyist 3D printers that use ABS plastics as
substrates. Full colour 3D printers are still prohibitively
expensive (and large) for individual use, and are thus
typically housed in commercial and academic facilities.
7 Y. Li and A. H. Flood, Angew. Chem., Int. Ed., 2008, 47,
26492652.
8 S. Lee, C.-H. Chen and A. H. Flood, Nat. Chem., 2013, 5,
704710.
9 Freely available for Linux, MacOSX and Windows operating
systems, from: http://www.ccdc.cam.ac.uk/Solutions/CSDSystem/
Pages/Mercury.aspx. Last accessed on February 11, 2014.
10 Blender is free software, available for Linux, MacOSX and
Windows operating systems at: http://www.blender.org/download/.
Last accessed on February 11, 2014. Blender is convenient
to use because of the wealth of user documentation freely

This journal is The Royal Society of Chemistry 2014

View Article Online

Open Access Article. Published on 04 April 2014. Downloaded on 26/03/2015 00:35:55.

This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence.

CrystEngComm

available online, which is further complemented by numerous

YouTube videos illustrating individual features. This body of
helpful information should make troubleshooting easier for
the users of our procedure.
11 Freely available at: http://epmv.scripps.edu/download-installfree/installers/. ePMV is available for Linux, MacOSX and
Windows operating systems. Last accessed on February 11,
2014. Note thatat the time of this writingePMV
operates on Blender 2.62, which is not the same as the
latest version of the program (Blender 2.69 for Windows
and Blender 2.70 for MacOSX). Therefore, both versions
of Blender should be downloaded and used, which is
fortunately possible. It is reasonable to assume that these
functionalities will eventually be combined in a single

This journal is The Royal Society of Chemistry 2014

Highlight

version of the program, which would simplify our procedure.

See also: G. T. Johnson, L. Autin, D. S. Goodsell, M. F. Sanner
and A. J. Olson, Structure, 2011, 19, 293303.
12 http://www.shapeways.com.
13 Material Safety Data Sheet (MSDS) for Full Color
Sandstone can be found at: http://www.shapeways.com/
rrstatic/material_docs/m-sds-sandstone.pdf.
14 For comparison, building a model of MOFF-3 similar to the
one shown in Fig. 3, but using modular commercial molecular model kits would cost approx. $300. In addition, these
sizes of atoms in these kits are too large to make them practical for MOF structures with numerous atoms; thus, a single
unit cell model for MOFF-3 would be 30 30 30 cm large.
3D Printed models permit much smaller feature sizes.

CrystEngComm, 2014, 16, 54885493 | 5493