Macs in Chemistry

Insanely Great Science

3D printing

ChemDoodle 3D v6.5: 3D Printing


Whenever I post anything on 3Dprinting it always generates interest so this update of ChemDoodle 3D will probably be of wide interest.

Export your ChemDoodle 3D creations into many popular 3D model file types for import into other CAD applications and for 3D printing:

  • 3D Manufacturing Format {.3mf}
  • Additive Manufacturing File Format {.amf}
  • COLLADA Digital Asset Exchange {.dae}
  • Extensible 3D Graphics {.x3d}
  • Polygon File Format {.ply}
  • STereoLithography {.stl}
  • Virtual Reality Modeling Language {.wrl}
  • Wavefront Object File {.obj}

A new method for 3D printing


Where as the usual 3D printing methods create a 3D object by printing it layer by layer a recent publication in Science DOI described a method by which the objects were created by passing light through liquid acrylate. Computed Axial Lithography (CAL), allows generation arbitrary geometries volumetrically through photopolymerization. The process was inspired by the 3D image construction used in CT scans.

The exposure process takes about two minutes for an object a few centimetres across; the team recreated a version of Auguste Rodin’s sculpture The Thinker a few centimetres tall.

The supplementary materials include details for printing several objects

I've added it to the 3D printing page.


Three-Dimensional Printing of Ellipsoidal Structures Using Mercury


A recent paper on ChemRxiv

A description of how to use the Mercury software from the CCDC to print 3-dimensional crystal structures that depict the anisotropic displacement parameters, matching the commonly used ellipsoidal depiction used in scientific papers. Details on how to convert a cif file into a 3D printing data file is included in the main paper, and details on the preparation of that data file for printing on a number of different 3D printers is included in the ESI.


There is more on 3D printing here .


3D printing large models


Whilst I've seen lots of examples of printed small models this is the first time I've seen an example of models suitable for using as teaching aids in a lecture theatre, excellent idea.

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.

Now added to the 3D-printing page.


HP says 3D printing is moving from niche to production


The 3D printing page always attracts a regular stream of readers so I thought I'd flag this article from HP.

Digital manufacturing with 3D printing has the potential to disrupt the $12 trillion global manufacturing sector, said Timothy Weber, HP vice president and general manager of 3D materials and advanced applications.

HP began shipping its model 4200 Multi Jet Fusion units with Voxel-level 3D printing, that has a 21-micron resolution.


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


A while back I mentioned a JMOL script for creating files for 3Dpriting the paper desiring the work has now been published in Journal of Cheminformatics DOI.

Three-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.

The Jmol 3D Print website allows the creation of STL and VRML files for 3D printing for any structure in the Open Crystallography Database. You can search either the full COD and then design your own model for printing, or search the more than 30,000 predefined sample files in the figshare collection and download the STL or WRL files that have already been created for those structures.


There is more information on the 3D printing page


Script for 3D printing from Jmol


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.


MOE 2016.08 released


Chemical Computing Group have just announced an update to MOE. This release has fixed a couple of Mac OSX 10.12 (Sierra) issues but also brings a host of new features.

  • MOEsaic: Web-Application for Ligand Analytics
  • Spectral Analysis for Structure Determination
  • Enhanced Protein Patch Analyzer
  • Integrated Antibody Project Database and Antibody Homology Modeler
  • Small Footprint MOE to Facilitate Large Scale Deployments
  • Physical and Virtual Rendering of Structures

A more detailed description of the new and enhanced features in MOE 2016.08 can be found at


3D Printing


I’ve updated the 3D printing page to include Chemtube3D which has a number of chemical reaction transition states in both the .stl and .x3d format which work with most printers.

A list of available transition state classes is shown below:

  • (C=O) Nucleophilic Substition and Addition
  • Pericyclic and Diels-Alder Reactions
  • Heterocycles
  • Rearrangements
  • Radical and Stereospecific Reactions
  • Organometallic Reactions  


3D printing


The page I wrote on 3D printing has proved to be pretty popular so I thought I'd mention that the NIH 3D print exchange has been updated with new features to improve printability.

AstroPrint is a neat way to slice, store, and manage your print files in the cloud. The service works by taking your uploaded 3D model, adding supports, slicing it, and saving the gcode in your account online. You can then access, download, and print your models. It's like a combination of 3D printing software, such as Cura or Repetier Host, with cloud storage.


A cloud-based 3D mesh repair application from Netfabb. Sometimes the mesh of a model can contain errors that are hard to find, and even more difficult to fix. Holes, inverted normals, intersecting faces, and isolated pieces can all cause problems during 3D printing. These mistakes can occur frequently when models are generated from "messy" datasets, such as image stacks or CT data.


3D printing improvements


3D printing has become a useful way to produce representations of scientific objects of interest, whether it be small molecules binding to a target protein to complete organisms.

Traditional 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. This is a time-consuming process but a new process described in Science DOI aims to reduce production times considerably, at first examination this looks to be a real game changer.

We demonstrate the continuous generation of monolithic polymeric parts up to tens of centimeters in size with feature resolution below 100 micrometers. Continuous liquid interface production is achieved with an oxygen-permeable window below the ultraviolet image projection plane, which creates a “dead zone” (persistent liquid interface) where photopolymerization is inhibited between the window and the polymerizing part.

The authors have formed a company to exploit the new technology carbon3D, the website gives more details on the technology.


More on 3D printing


The NIH 3D Print Exchange now has over 460 models available for printing, ranging from small molecules to proteins and macromolecular assemblies to anatomical models. There are also an increasing selection of lab ware, including small flasks and racks.


There are more resources details here.


3D printing molecules


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 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.

I’ve also updated the 3D printing page to include several new resources.