We have been experimenting with full-colour 3D printing of molecular objects. I thought I might here share some of our observations. Firstly, I list the software used:
My first attempt was to 3D print a molecular orbital; in fact the one shown in this post. To be printable, a 3D object must be fully connected, in other words not contain any disconnected components. To ensure this is true for a molecular orbital, one has to select a very low isosurface threshold; 0.005 au in this case. The orbital is computed as a Gaussian cube, and converted to a .wrl file as follows
isosurface sign color yellow green cutoff 0.005 "144.cub"
write model.wrl
set exportScale 8.0
exportscale
against the resulting printing price to get the desired result (by trial and error, but perhaps there is a more systematic way of doing this?). One of my colleagues (Paul) has had this sort of thing printed to about 25cm in size for about this price, and the model seems reasonably robust to physical handling. It may also benefit by fine-tuning of the bond radius; thicker would clearly be stronger.‡If anyone reading this post has their own experience of 3D colour printing of chemical models, do please post comments here. And I dare say that in a few years time, students will simply press the “3D print” button on the tablet they are using to view lecture notes to get a copy. Mind you, I am somewhat ambivalent about such a process, having spent the last twenty years trying to discourage students from using the “2D print” button on their computer. Will I eventually come to adopt the same attitude to 3D print (if you click on the MO image above, you will get a virtual 3D model instead of a physical one).
‡ The width of a bond can be set using the Jmol command: set bondRadiusMilliAngstroms 300
This post has been cross-posted in PDF format at Authorea.
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Lee Cronin has reported 3D-printed reactionware with printed-in catalysts.
Here's a fun idea: Catalyst printed into a model of the catalyst.
Just pluck the model of the catalyst you want to use out from the display cabinet and dunk into the reaction. When your done, simply pluck the model out of the reaction mixture, give it a rinse and a little shake, and place back in the display cabinet.
By the way, Shapeways accept the more modern X3D file format, which can also be written by Jmol.
> write X3D "fileName"
Re: X3D, yes they accept a variety of formats. But I can see no obvious benefit of using X3D vs WRL; they seem entirely equivalent (and so they should, X3D is simply an XML serialisation of WRL).
Do you have a doi for Cronin's work?
The idea of a library (cabinet) is good. We actually have such a cabinet in the entrance to our chemistry dept. It contains 3D models of molecules, but embedded in lead crystal glass (and in monochrome). No doubt some of the models I have printed will find their way in!
Integrated 3D-printed reactionware for chemical synthesis and analysis: 10.1038/nchem.1313
Six π-MOs from benzene: http://shpws.me/oYY1 http://shpws.me/oYY6 http://shpws.me/oYYa (occupied) http://shpws.me/oYYh http://shpws.me/oYYk http://shpws.me/oYYp (unoccupied) and four from cis-butadiene: http://shpws.me/oYZa http://shpws.me/oYZd (HOMO), http://shpws.me/oYZn (LUMO), http://shpws.me/oYZp were generated following the procedure outlined above (the costs relate purely to manufacturing, with no percentage given to the designer!). They will be used in my undergraduate lectures (time will tell whether they are robust enough for an enthusiastic student audience).
Henry,
Do you think it is feasible to use MRI, CAT and X-ray to create accurate 3-D models of hip joints (or indeed any other joint) and using carbonated compounds or structurally comparable biomaterials recreate via 3D-printing? Would ceramic derivatives be compatible with the molecular 3D printing process and would the chemical bonds created be sufficiently strong to manage body weight and the full range of movement (wear and tear etc). Many thanks.
I can only answer the previous question by saying the learning curve is actually both steep and extensive. We have looked at a variety of different machines used to 3D print in a variety of materials. Modern printers nowadays can manufacture in several materials, either consecutively (depositing one on the other) or at the same time. They can even blend a continuously varying mixture of polymers.
I cannot answer your questions, but I do strongly suspect that this area (like other technologies such as eg mobile phones) is going to advance very rapidly indeed over the next decade.
Can you lay out color setting commands in the Console. I think we can try making a model in Chem3D from Chemdraw and save the file into .PDB file which can be opened and saved as .wrl in JMol. What i can't do is to render colors for each atom/atom types. Help would be appreciated.
Thanks
Mahender
Atom colours can be set using the standard Jmol commands, documented here: http://chemapps.stolaf.edu/jmol/docs/#coloratomobject.
Hi, I used your instructions to create this Tryptamine model as a going away gift to my adviser! Thank you!
https://www.shapeways.com/model/1623207/gpyout.html?li=aeTabs