Before you read, note that I have not yet successfully printed a protein’s ribbon-structure on our lab’s Form 1+ machine. I’m asking for help in getting this working. Thanks in advance for reading my post.
Edit 2: Significant progress has been made. One user has been able to print the protein on his Form 2. He, along with others, have provided some great tips and feedback for how to get this done. Their responses are also great advice for printing in general on formlabs machines. On my third print with our Form 1, I have had some success but am still looking to improve the results. Thanks again for checking out this thread, and a big thanks to all those that’ve responded.
We are interested in 3D printing the ribbon structure of proteins and our lab has a Form 1+ printer. Our first protein we’d like to print can be found here on the NIH 3D Print Exchange:
As explained there, we downloaded a .pdb of our protein and swapped one molecule inside it, saving this new file as a .pdb as well. We then uploaded the .pdb to the Exchange, which converted the .pdb into .stl and .wrl files. The Exchange uses Netfabb to repair holes and other errors to ensure that we have printable files. Finally, we downloaded from the exchange one of the .stl files and opened it in the PreForm software.
File downloaded: 2hi4zcafdocked1-ribbon.stl
Below is what our protein looks like in the software:
And below is what it looks like all ready to print. We kept the scale at 1.00, and used auto-orient to arrive at the tall and skinny structure. For the supports, a colleague suggested a Density of 1.24mm and Point Size of 0.4 mm. We used the generate supports feature, and added supports for red areas.
Note: There was one small red area that even after adding 4 supports to it did not remove the red shading. We added one extra support and ignored the red shade there.
We printed with the medium print resolution (0.05mm layer thickness) with white resin (FLGPWH01). It was a 5-hour print with 1381 layers and 29.90mL resin to be used. Below is our result.
That was not a good print.
Note: before we printed the protein, we did a test print to be sure our machine was working and it printed as expected.
Brainstorm: What went wrong with our first print?
- Not a machine issue, we checked that with a test print
- Not a corrupt file, the Exchange used Netfabb to fix the errors
- Maybe the print size was too small, and the thickness of the protein ribbon structure too thin.
- Maybe the active site had too many molecules and was too complex.
- Maybe we used too many support and it made the print too complex.
- Maybe the print was oriented in an awkward way, making the print too complex.
Okay, so we had a checklist for what we wanted to change for the second print. The print size, support density, and orientation could all be changed in the Preform software. Simplifying the active site of the protein required another program that could manipulate .stl files.
After some web-surfing, I downloaded Meshmixer and imported the 2hi4zcafdocked1-ribbon.stl file into it. The active site of the protein is like an internal cavity. It has two molecules that I want inside, which are attached to the protein via support rods. It also has molecules (amino acid residues) sticking out of the protein, about a dozen or so. I don’t really want these. With Meshmixer, I was able to literally slice those molecules off the protein, and delete them from the file.
Here’s what it looked like before in Meshmixer:
and here’s what it looks like after slicing:
Note: I also added some rods connecting the heme’s iron to the heme’s porphyrin ring. A little handy-work on my part, I don’t think it foiled the print though.
The slicing was a bit crude, but I figured I could address the stumps post-production. With that done, it was back to the PreForm software.
I scaled the file 1.75 times the original file size and used auto-orient a couple times and decided upon a flat orientation for the protein. This time when we generated supports, we used a density of 0.5 and point size of 0.4mm. There were no red areas this time around, was it too good to be true?
Again, we printed with the medium print resolution (0.05mm layer thickness) and white resin (FLGPWH01). Print time was about 9 hours, with 1686 layers and 82.45mL of resin to be used. Nothing was printed after the first print and before this second print of the protein. When preparing the tank, I did notice a small dot (size of a dull pencil tip) of cloudiness in the tank, but it was faint and I decided to continue on with the print.
Here was the result of our second print:
No good, again!
Upon cleaning the device, I scraped off this piece of resin from the bottom of the tank.
I also noticed a significant cloudy area (a little less than 1/9th the tank) in the center of the tank’s base. I don’t know how old the tank is. We are currently ordering more tanks.
At this point, I looked on the forums and surfed the Internet to see if others had some advice or clues to what I could do next. But alas, there is no thread about printing ribbon-structure models of proteins with formlabs 3D printers. I’m interested in getting this working for the Form 1+ if possible.
I don’t know what the problem is. I’m thinking it’s something to do with the supports. My next steps might be to simplify the design in order to see what prints well and what does not.
If you have any comments, questions or suggestions, please respond! I hope we can figure this out.