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Monthly Archives: October 2012

Introduction

I had theorized in my previous post that it was possible to easily 3D print an enzyme structure given a Protein Data Bank (PBD) file. Now, a month and many iterations later, I was finally able to print restriction enzyme Fok1 [PDB ID:1fok], bound to a strand of DNA. I had not anticipated the problems of 3D-printing such a complex structure when I first started this expedition, I now have a very robust and simple way of printing these structures.

3D printed Fok1 in hand

Result

3D-printed Fok1

The printed model, Fok1 [PDB ID:1fok], is in Sculpteo’s white plastic, and is approximately 4.8cm x 4.0cm x 4.3cm. It has a slight coarse and grainy texture, but still retains tiny details like arrowheads on the model. One factor that surprised me is the model’s flexibility. Whereas my previous printed models were rigid, this printed protein strand has spring like behavior in certain areas and can withstand some serious stretching.

Method Summary

My goal was to optimize simplicity in the PDB-to-3D-model methodology. This means, I wanted minimal manual adjustment of vertices to the PDB render. On top of that, I wanted to print a ribbon style model, which was more challenging to print than a mesh based model, due to its thin components.

I started by rendering the Fok1 [PBD ID:1fok] in Chimera. Chimera conveniently can export the model in a STL format, perfect for 3D printing. Before exporting, I thickened the model to meet minimum thinness requirements. Finally, I uploaded the STL to Sculpteo to print.

Sculpteo Render

Fok1 model on Sculpteo

Method Details

  1. Import PBD file into Chimera, via either a fetching of the file from PDB or a custom PDB file.
  2. Select the chains containing DNA or substrate and hide the atom and bond models. The atom and bond models typically are too thin to be printed, without more finessing.

  1. Select the remaining ribbon model and adjust the ribbon model attributes in Tools>Depiction>Ribbon Style Editor. The ribbon model, as is, is too thin to be printed. All attributes need to be thickened. The following is the setting I used for my Fok1 model.

Ribbon Style Editor Settings

  1. Export the scene to an STL and then upload the model to Sculpteo for printing. Sculpteo offers a beautiful, almost-real-time printability check of the model, for fast design feedback turnaround times.

Caveats

The major problems I encountered was having structures too thin to be printed. I initially tried to print with Shapeways. However, the first ~10 iterations didn’t even pass their manual checking stage. Printing a wirely protein structure is definitely pushing the boundaries of 3D printing capabilities. I eventually decided to switch to Sculpteo because of their significantly faster turnaround times. Sculpteo was awesome and definitely delivered.

Sound the trumpets!

The megalopolis is back!

One one fine weekend in September, a friend and I hiked far into uncharted lands for Magic’s Return to Ravnica pre-release event. We each pledged a guild. I applied for the Azorius Senate, beholder of justice and law. He joined the ranks of Rakdos, bringer of pain.
rtr
We played epic games nonstop till the late evening. Even though I didn’t fare as well as he did, I was able to summon my Utvara Hellkite in a couple of matches. It always brought me a smile watching my opponent quiver in its wake.
hellkite
The pre-release was exceptionally fun. I saw a few of the people I’d met at Friday Night Magic, and was surprised by a long-ago friend attending as a referee. Magic events just keep on getting better.

Wow.
It’s been a while since I updated.

Life has been full of epic adventures.

Just a few weeks ago, my summer roomies Aaron and Jeff moved out, and my olde roomies Stephie and Tom moved back in.
Stephie and Tom
We had an epic dinner night where I made accidentally-too-spicy lasagna, sending us all reaching for jugs of water one after another.
spicy
Jeff, soon after moving into his hip new dwelling, invited a lot of his friends to a delicious end-of-summer barbeque. There were tons of impressively delicious food.
skewers
That night must’ve been party night of the year, because everyone we knew was raising their apartment roofs. We shuttled to and pro from Boston for a evening of fun gatherings. Afterwards, we returned to Jeff’s for hopscotchin’ sofa-jumpin’ games.
couch
Crazy fun times.

More to come.