Macs in Chemistry

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3D Printing

3D printing is a process of making a three-dimensional solid object of virtually any shape from a digital model and I guess it is a sign that what was a bleeding edge technology has now become mainstream when the London branch of Selfridges announce that the team at iMakr, a 3D printing workshop based in Clerkenwell in London are opening an in store studio. 3D printing uses an additive process, where successive layers of material are laid down in different shapes to slowly build up the final 3 dimensional shape.

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Image generously provided by Molecular Graphics Laboratory, The Scripps Research Institute

File Formats

There a wide variety of file formats however some of the older formats do not support colours or textures, unfortunately the latest update to Chem3D for iPad can only export in stl format which does not support colours.

File Format 3D
Geometry
Colour
Support
Texture
Support
3DS (3D Studio) Yes Yes Yes
AC3D Yes Yes Yes
ASE (3D Studio) Yes No No
COB (TrueSpace) Yes Yes No
DAE (Collada) Yes Yes Yes
DXF4 (AutoCAD) Yes Yes No
IGES Yes No No
KMZ (Google Earth) Yes Yes Yes
LWO (LightWave) Yes Yes Yes
MD2/MD3 (Quake) Yes No No
OBJ (Wavefront) Yes Yes Yes
OFF Yes No No
PLY (Standford) Yes Yes No
Q3O (Quick3D) Yes Yes Yes
RAR3 Yes Yes Yes
SCAD (OpenSCAD) Yes No No
SKP (Sketchup) Yes Yes Yes
STEP (ISO 10303) Yes No No
STL Yes No No
TGZ3 Yes Yes Yes
VRML Yes Yes Yes
ZIP3 Yes Yes Yes

Modelling Software that supports 3D output

A number of applications can be used to create the files required for 3D printing,

It is important to note that the structures need to be a single non-disconnected model, it may also be necessary to add scaffolding struts to support the model during the printing process, these can be removed later.

Section 3 of the Jmol user guide gives step by step commands needed to design a model that will be built on a 3D Printer

There is a Youtube video that demonstrates how to export a file from JMol, edit it in Blender and then submit to Shapeways for printing

Henry Rzepa has detailed his exploration of 3D printing from Jmol on his blog.

There are instructions for using PyMol here

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Image generously provided by Molecular Graphics Laboratory, The Scripps Research Institute

Useful Resources

Scripps Physical Model Service A service providing 3D models maintained by Adam Gardner that was started by Prof. Art Olson of the Molecular Graphics Laboratory at The Scripps Research Institute, the structure needs to be in PDB format or a variety of 3D model formats. Adam is also an invaluable resource for answering questions!

Center for BioMolecular Modeling resources for teachers

3D Printing Crystallography Community Home

AccuTrans 3D 3D file conversion programs

Blender open source tool for file conversion and manipulation.

Chemtube3D has a number of chemical reaction transition states in both the .stl and .x3d format which work with most printers.

MeshLab open source tool for file conversion and manipulation.

Netfabb file checking and repair.

NIH 3D Print Exchange an open, comprehensive, and interactive website for searching, browsing, downloading, and sharing biomedical 3D print files, modeling tutorials, and educational material.

Shapeways Online printing service

Sculpteo file checking, repair and robustness check and printing.

A Jmol Script for Programmatic Conversion of Crystal Structures into 3D Printable Files can be downloaded here created by Vincent F. Scalfani, Antony Williams and Valery Tkachenko.

There is also a detailed video.

There was an interesting presentation at the 248 ACS Meeting Accessing 3D Printable Structures Online Vincent F. Scalfani, Antony J. Williams, Robert M. Hanson, Jason E. Bara, Aileen Day, and Valery Tkachenko Science and Engineering Librarian, The University of Alabama vfscalfani@ua.edu 248th ACS National Meeting San Francisco, CA August 13, 2014 slideshare describing the construction of the RSC Crystal Data Repository of crystal structures all of which can be downloaded in a format suitable for 3D printing. Currently contains: the entire Crystallography Open Database (COD) of 289,395 .cif and 48,022 .hkl files of molecules and extended solids; 3D Printable Files – 31,239 .wrl files (color printing) and 11,732 .stl files. 3 Still in beta mode, can manually browse through files. Repository will soon have user interface that is fully searchable (name, structure, formula, SMILES, InChI, and others) with deposition and crowd-source curation/ annotation platform.

Fabrication approaches for the creation of physical models from microscopy data DOI A description of 3D printing from optical imaging methods, such as confocal microscopy and multiphoton microscopy. The creation of the models, discussed here, highlight similarities that can be applied to create models from many microscopy techniques including electron microscopy and other optical modalities.

Three-Dimensional Printing of a Scalable Molecular Model and Orbital Kit for Organic Chemistry Teaching and Learning DOI

Three-dimensional (3D) chemical models are a well-established learning tool used to enhance the understanding of chemical structures by converting two-dimensional paper or screen outputs into realistic three-dimensional objects. While commercial atom model kits are readily available, there is a surprising lack of large molecular and orbital models that could be used in large spaces. As part of a program investigating the utility of 3D printing in teaching, a modular size-adjustable molecular model and orbital kit was developed and produced using 3D printing and was used to enhance the teaching of stereochemistry, isomerism, hybridization, and orbitals. largemolskit

Updated 3 August 2018