[Chimera-users] 3D Printing our protein

David Bhella david.bhella at glasgow.ac.uk
Sun May 19 23:37:35 PDT 2013

Hi Bart
I have printed several cryoEM 3D reconstructions that I exported from Chimera as VRML, using the online 3D printing agency shapeways. They have some useful advice on fixing models so they are suitable for 3D printing using two free programs meshlab and netfabb.


It worked well for me, meshlab may help you reduce the size of your model, while netfabb repairs the surfaces, ensuring they are manifold...


On 20 May 2013, at 02:23, Bart Janssen <Bart.Janssen at plantandfood.co.nz> wrote:

> Hi
> My apologies for what are likely to be stupid questions. We are plant developmental biologists and we just obtained our first X-ray crystal structure for a new hormone receptor in plants. We’d really like to make a 3D model of the protein using one of the 3D printers at our institute.
> I’ve been trying to use and understand Chimera for the last week and I’m a bit out of my depth :). I can import our protein 4DNP.pdb and display it using solid surface or using the sphere representations of atoms. I can also display it with the “lid” domain hidden and vice versa.
> My problem has been getting files that our 3D printer can read. The solid surface model of the whole protein can be exported as a scene in .stl format and that can be printed just fine. Although I can’t figure out how to adjust resolution or the smoothness of the exported file.
> But I’d really like to print the two domains of the protein separately. If I use Solid surface model with the lid hidden what I get is an eggshell like model which has no internal detail. If I use atoms shown as spheres instead I get the internal detail I want BUT when I try and export the scene I get a 2 Gb+ file that is unreadable by the printer. If I export .obj format instead the colleague who runs the printer says the file won’t load and appears to have errors.
> I have a horrible feeling I am going about this entirely the wrong way but I can’t find a tutorial that describes what I’m trying to achieve. I do realise chimera is not really written for the somewhat trivial use that I am attempting but it really would be helpful if we had a physical model of the protein to look at.
> Is there a tutorial I should follow or another part of Chimera (or another program) that I should be using instead? Any advice would be much appreciated.
> Cheers
> Bart
> Bart Janssen
> Scientist
> Plant Development team
> Breeding and genomics
> Plant and Food Research
> Private Bag 92169
> Auckland 1142
> New Zealand
> Ph +64 09 9257179
> bart.janssen at plantandfood.co.nz
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