Where we left off…
Hello again to those reading the blog. It has been a complete struggle with the multi extruder going from issues galore to straight up malfunctioning. Point being I have made basically no progress with the multi extruder, and I plan to try my best to get something over the next few weeks. Regardless, to keep moving forward I have been mostly working with CAD to figure out a good way to interconnect multi-subunit structures. I have already printed one of the designs and I feel pretty good about how it came out.
First off check out those organic supports… even if they didn’t improve the efficiency of printing, I would use them, I mean look at how cool they look.
There are many parameters that have changed since when I first started printing these structures and I think for those who are trying to replicate this process it would be good to go over each change separately. Furthermore, there are many steps to this process that I never touched on and those will also be listed here as well.
Where and how to find STL files of 3D molecular structures…
Where: I have always taken STL files from a website called the Protein Data Bank (rcsb.org)
Finding STL Files:
- To obtain a molecular structure STL file you must first assign a 3D representation to the molecule of choice. This can be done after moving to the “Explore in 3D” window.
- When you are able to view your desired structure in 3D, we are then able to edit the 3D representation of the molecule. This is done under the “Add Representation” setting which is under “Components”
- Note: Ensure you remove all of the previous representation that were assigned to the model prior to exporting the STL file. If this step is skipped, the compounding representations cause issues during printing.
- Note: I have always used the “Gaussian Surface” or “Molecular Surface” representation for my prints, but I did find the “Gaussian Surface” representation prints more cleanly (Even though I think Molecular Surface looks way better 🙁 )
Note: Noticed how there are both “Cartoon” and “Gaussian Surface” representations present for the polymer. If you look closely there are sections where the cartoon representation (ball and stick) is sticking out of the Gaussian surface.
- After the representation is assigned to your Polymer (molecule) it may be in your best interest to delete the “water molecules” and ligands (unless you wish to print these as well in which case you will have to edit the ligands representation in the same fashion as stated in the last step).
- Finally scroll down to “Export Geometry” as an “STL file.”
What 3D-Printing Software do I use and what settings have I changed from default…
Software: At my university we use Prusa printers and have therefore opted to use the Prusa software for 3D-printing. Keep in mind that any 3D-printing software can be used to have a similar effect, however I cannot promise the information I have provided transfers.
Changes to settings: (At this point 11/11/24)
- One of the main changes I made to my printer settings was the use of “Organic” supports. This was a fairly recent development for me however for the particular models I am printing it makes a huge difference.
- Note: Regardless of how nice the organic supports are, soluble supports are still vastly superior.
- Making minor adjustments to extruder/heat bed temperatures (increasing if clogging is an issue or decreasing if the print quality seems reduced; i.e drooping).
- Other support settings that I have changed with variable rates of success include: reduction in “Top Interface Layers,” changing the support “Pattern,” and changing the support “Interface Pattern.”
I have gone into more detail concerning most of these changes on other blog posts so check there if you are interested.
The New and Improved?…
Now that we got that out of the way I can discuss the progress I made over the last couple of weeks. I have been working with a molecule called hemoglobin during my last few prints and this is not without reason. Hemoglobin is the oxygen carrying molecule that resides in our blood which is composed of 4 subunits (typically 2 alpha and 2 beta subunits however there are some forms that are 2 alpha and 2 gamma). Of these 4 subunits each contains what is referred to as a protoporphyrin ring which is a complex ring structure that contains an iron center which is responsible for binding molecules like oxygen, carbon monoxide, and other molecules like 2,3-BPG. The 4 subunits of hemoglobin are folded into a quaternary structure that is formed through multiple hydrogen bonds and disulfide bridges. I know that sounds like a bunch of nonsense, but all of these characteristics of hemoglobin can be represented in a single 3D molecular representation. The bonding between subunits will be represented with pegs in some precise locations (not all as that would be crazy) and the distinct protoporphyrin rings can be shown using a disk that slides in and out of the model. That was a long-winded explanation but here is the final product…
Notice the disks. These are the disks that represent the protoporphyrin ring systems. There are only two just because I just wanted to test an idea. Also, later on these will be a different color to the base model.
What’s Next…
These next few weeks are exciting as we have received a shipment of new PVA filament for soluble supports. The last batch seemed to have gone bad as large segments of the filament absorbed too much moisture. We also purchased a 3D filament dryer which I would highly recommend to anyone that plans to take on larger 3D printing projects.
Furthermore, I plan on switching to a new design a new molecule called BCR-ABL. Now if you want to explore this before my next post GO FOR IT. I will be providing a semi-in-depth explanation of what this protein is, why is it a good protein for 3D modeling, and how it related to chronic myeloid leukemia (CML) in my next post. Oooooo, sneak peek I know… exciting.
