One-click preparation of 3D print files (*.stl, *.wrl) from *.cif (crystallographic information framework) data using Cif2VRML

Kaminsky, Werner; Snyder, Trevor; Stone-Sundberg, Jennifer; Moeck, Peter

doi:10.1017/s0885715614001092

Cited by 20 publications

(22 citation statements)

References 22 publications

(28 reference statements)

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“…Similarly, the Cif2VRML application does not remove solvent molecules (except for biomolecules) or counterions, does not apply symmetry, and does not automatically select a particular structure for representation. Several of these options are reported to be included in a future release of the Cif2VRML application [18]. …”

Section: Resultsmentioning

confidence: 99%

“…There are currently only two methods available for programmatic conversion of a crystal structure into a 3D printable file including the NIH 3D Print Exchange web tools developed by Coakley and coworkers at the NIH [15–17] and the stand-alone Cif2VRML Windows application developed by Kaminsky [18]. The NIH 3D Print Exchange web tool uses Chimera [12] and Blender [19] scripts that automatically process crystal structures into 3D printable files.…”

Section: Introductionmentioning

confidence: 99%

“…The NIH 3D Print Exchange Team has made all scripting code available in the public domain, so researchers could adapt these scripts to programmatically process multiple files locally in the future [16]. Multiple file processing is also not currently available in the Cif2VRML application, but is being considered in a future release [18]. …”

Section: Introductionmentioning

confidence: 99%

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Programmatic conversion of crystal structures into 3D printable files using Jmol

Scalfani

Williams²,

Tkachenko³

et al. 2016

J Cheminform

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BackgroundThree-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.ResultsA collection of over 30,000 crystal structures in crystallographic information file (CIF) format from the Crystallography 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.ConclusionsOver 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 created 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 converting large database collections of crystal structures into 3D printable files.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Programmatic conversion of crystal structures into 3D printable files using Jmol

Scalfani

Williams²,

Tkachenko³

et al. 2016

J Cheminform

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show abstract

“…Since ORTEP, numerous visualization programs for molecules and crystal structures have been developed (e.g. PLUTO , RasMol , Mercury , Jmol , GRETEP , Cif2VRML and many more) that give not only 2D representations of 3D molecules and structures, but also interactive capabilities such as rotating, selecting the number of unit cells displayed, and multiple viewing options, e.g. Figure , that can include ball‐and‐stick, space filling, coordination polyhedra, and ribbon representations of amino acid sequences.…”

Section: A Brief History Of Crystallographic Information Representationmentioning

confidence: 99%

“…Screenshot of the Cif2VRML software with a caffeine molecule model that was created from CIF data (*.cif). This program was used by our group extensively to generate 3D print files (*.wrl and *.stl).…”

Section: A Brief History Of Crystallographic Information Representationmentioning

confidence: 99%

3D printed models of small and large molecules, structures and morphologies of crystals, as well as their anisotropic physical properties

Stone-Sundberg

Kaminsky

Snyder

et al. 2015

Crystal Research and Technology

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Three-dimensional (3D) physical models of atomic structures of crystals, their anisotropic properties and morphologies as well as models of small and large molecules were printed with support from 3D Systems Corporation. Structural information in Crystallographic Information Framework (CIF) files from the Crystallography Open Database and the Protein Data Bank was utilized. Computer programs were either newly developed (Cif2VRML) or enhanced by 3D print file export functions (WinXMorph and WinTensor) in order to design most of these models. Current 3D printing technologies are briefly reviewed. The literature on the impact on students' comprehension and retention of structural information with access to such models is assessed. Our taking of a historical perspective in this paper illustrates that the usage of models has for more than 200 years been an integral component of crystallography.

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Crystallography Open Database: History, Development, and Perspectives

Gražulis

Merkys

Vaitkus

et al. 2019

Materials Informatics

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One-click preparation of 3D print files (.stl, .wrl) from *.cif (crystallographic information framework) data using Cif2VRML

Cited by 20 publications

References 22 publications

Programmatic conversion of crystal structures into 3D printable files using Jmol

Programmatic conversion of crystal structures into 3D printable files using Jmol

3D printed models of small and large molecules, structures and morphologies of crystals, as well as their anisotropic physical properties

Crystallography Open Database: History, Development, and Perspectives

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