Shapeways is one commercial company that can produce full-colour 3D-printed models. As we start to generate such content, it is desirable to try to keep track of what is available from local activity (the Shapeways catalogue already contains much chemistry). The list below illustrates some of this activity:
The MOs of Copper phthalocyanine HOMO, mauveine (HOMO and LUMO) and an octaphyrin (corresponding to the artwork on the student resource-centre windows)
The NBO orbitals showing the overlap leading to the gauche effect in 1,2-difluoroethane.
>isosurface sign color yellow green cutoff 0.02 bd_mol15.cub
>set exportscale 12.0
>write bd_mol15.wrl
Upload the .wrl file to the manufacturer
You should replace the values above with ones relevant to your model. The isosurface cutoff can be adjusted to produce a good-looking model. Similarly the bond radii and the atom size (CPK). The exportscale controls the cost of the resulting model. If printed in full-colour sandstone, a model with largest dimension ~15 cm is going to be a reasonable cost.
An alternative output format which is accepted by some manufacturers is .obj. This produces not a single file but two or even three. These have to be zipped into a compressed archive before uploading.
Instructions on how to generate 3D-printable models (ball&stick) using Jmol.
Acquire suitable coordinates. If from a crystal structure, it is probably best to save as a .pdb file rather than .cif. Ensure you edit the connectivity to avoid any components which are disconnected from the main model. If necessary, connect them using an explicit bond.
An alternative output format which is accepted by some manufacturers is .obj. This produces not a single file but two or even three. These have to be zipped into a compressed archive before uploading.
Instructions on how to generate 3D-printable models (proteins) using PyMol.
Drag-n-drop a .pdb file onto the main Pymol Window (MacPymol tested). It will open in standard wireframe mode.
Edit off any water molecules and other disconnected units (skill needed here!)
From the all/S(how) button (right), select surface
From the all/C(olour) button, select spectrum (or other)
From File/Save image as/VRML 2, save a .wrl file.
Scale this file as per below using a text-editor to open the .wrl file.
Instructions on how to generate 3D-printable models (proteins) using Chimera.
Tools/Structure editing/Minimise structure offers editing tools to trim off solvent, non-complexed ions, incomplete side chains etc.
Actions/Surface/Show to produce a smooth Connolly surface.
tools/Depiction/Rainbow and select eg Residue.
File/Export-Scene and select eg VRML.
One can also load VRML (.wrl) files produced by other programs as a check.
Scaling a VRML file
Open the .wrl file in any simple text editor, and BEFORE the objects begin add lines:
Transform {
children [
At the very end of the file add
]#end of children
scale 2.0 2.0 2.0
}#end of Transform
An example might look like (the addition is just before the Shape command) for a scaling factor of 2.0 in all directions
#VRML V2.0 utf8
Viewpoint {
position 0 0 160.36393738
orientation 1 0 0 0
description "Z view"
fieldOfView 0.465421
}
DirectionalLight {
direction -0.348155 -0.348155 -0.870
}
NavigationInfo {
headlight TRUE
type "EXAMINE"
}
Transform {
children [
Shape {
.....
.....
]
}
}
] #end of children
scale 2.0 2.0 2.0
} #end of transform
Software
A variety of software for viewing, validating and editing the 3D models is available.
Chimera is very good for viewing a .wrl model on your computer after generation.
This company has a useful web site where you can colour-code the robustness of your model to manufacture. Red=likely to break; Green=robust, and hence adjust the bond thickness etc to the appropriate values.
Useful links
Macinchem have a very good collection of pointers.
