Category: Uncategorized

Wow, it’s been a while since I’ve written! However, if you’ve been on campus, you might have seen the lights up and running in the HCC. In blog post 6, I talked about the successful installation, so if you’d like to learn more, check it out!

If you read blog post 6, you may remember that I fried one of the boards on accident. We got a new one, and I wired it correctly this time. In this post, I wanted to address the wiring system I used in full. It’s a little complex, so bear with me.

The third floor wiring system is relatively simple. The lights have a voltage wire and a ground wire that connect directly to a power converter that plugs into the wall. The Elegoo Mega, my microcontroller of choice, is plugged directly into a separate power converter. Lastly, the two components (microcontroller and lights) are connected to each other by a ground wire and a digital wire, which connects to one of the digital pins on the microcontroller. The code calls out that specific digital pin and assigns lights to it. All in all, it’s four wires. Just don’t forget to connect the lights to a microcontroller ground pin- the digital pin puts out voltage and if you don’t close the loop, it will fry something. I’ll include resources if you want to learn more under the block of code!

The second floor wiring system is more complex than the one on the third floor, but only because of the second set of lights. Instead of requiring six wires, the second floor system uses eight. One set of lights is wired in the exact same way as the lights on the third floor, and the other set simply connects to a different digital pin and ground pin on the microcontroller. Just remember that each set of lights needs power (from the power converter) and data (from the microcontroller) and that every time a power or data wire is connected, a ground wire needs to be connected, too.

I’ll include a picture below, but it’s a bit difficult to see the wiring as it looks like a tangled mess. There’s a method to the madness, I promise!

Of course, it wouldn’t be an Evelynestallation blog post without a block of code, so I’ll attach the code the second floor lights are currently running. It’s a really pretty one- three rainbow comets, a pause, and then white sparkles. I enjoyed coding it, and I hope you enjoy getting to use it! The code for the third floor is similar. Just cut out everything marked with the number 2, and you’ll be all set.

#include <Adafruit_NeoPixel.h>
#ifdef __AVR__
  #include <avr/power.h>
#endif
#define PIN      5
#define PIN2     7
#define NUMPIXELS 300
#define NUMPIXELS2 178

Adafruit_NeoPixel pixels2(NUMPIXELS2, PIN2, NEO_GRB + NEO_KHZ800);

Adafruit_NeoPixel pixels(NUMPIXELS, PIN, NEO_GRB + NEO_KHZ800);

#define DELAYVAL 15
#define DELAYVAL2 50
#define DELAYVAL300 10 
#define BIGDELAYLOOP  12000


void setup() {
#if defined(__AVR_ATtiny85__) && (F_CPU == 16000000)
  clock_prescale_set(clock_div_1);
#endif

  pixels.begin(); 
    pixels2.begin();
 


}

void loop() {
  for (int g=0; g<12; g++)
{
  for(int i=0; i<NUMPIXELS; i++) {


    pixels.setPixelColor(i, pixels.Color(0, 0, 0));
     pixels.show();
   
    }
    for(int i=0; i<NUMPIXELS2; i++) {


    pixels2.setPixelColor(i, pixels2.Color(0, 0, 0));
     pixels2.show();
   
    }
  //rainbows comet loop
  
    for(int i=NUMPIXELS; i>-56; i--) {
 
   pixels.setPixelColor(i, pixels.Color(255, 0, 0));
   pixels.setPixelColor(i+1, pixels.Color(255, 62.5, 0));
   pixels.setPixelColor(i+2, pixels.Color(255, 127.5, 0));
   pixels.setPixelColor(i+3, pixels.Color(0, 255, 0));
   pixels.setPixelColor(i+4, pixels.Color(0, 127.5, 255));
   pixels.setPixelColor(i+5, pixels.Color(0, 0, 255));
   pixels.setPixelColor(i+6, pixels.Color(255, 0, 255));
   pixels.setPixelColor(i+7, pixels.Color(0, 0, 0));

 
 pixels.setPixelColor(i+60, pixels.Color(255, 0, 0));
   pixels.setPixelColor(i+61, pixels.Color(255, 62.5, 0));
   pixels.setPixelColor(i+62, pixels.Color(255, 127.5, 0));
   pixels.setPixelColor(i+63, pixels.Color(0, 255, 0));
   pixels.setPixelColor(i+64, pixels.Color(0, 127.5, 255));
   pixels.setPixelColor(i+65, pixels.Color(0, 0, 255));
   pixels.setPixelColor(i+66, pixels.Color(255, 0, 255));
   pixels.setPixelColor(i+67, pixels.Color(0, 0, 0));

   pixels.setPixelColor(i+120, pixels.Color(255, 0, 0));
   pixels.setPixelColor(i+121, pixels.Color(255, 62.5, 0));
   pixels.setPixelColor(i+122, pixels.Color(255, 127.5, 0));
   pixels.setPixelColor(i+123, pixels.Color(0, 255, 0));
   pixels.setPixelColor(i+124, pixels.Color(0, 127.5, 255));
   pixels.setPixelColor(i+125, pixels.Color(0, 0, 255));
   pixels.setPixelColor(i+126, pixels.Color(255, 0, 255));
   pixels.setPixelColor(i+127, pixels.Color(0, 0, 0));
   
   pixels.show();
   delay(DELAYVAL300*4);
    }
    
    for(int i=0; i<NUMPIXELS; i++) {


    pixels.setPixelColor(i, pixels.Color(0, 0, 0));
     pixels.show();
   
    }
    for(int i=22; i<NUMPIXELS2+NUMPIXELS2; i++) {
 
   pixels2.setPixelColor(i, pixels2.Color(255, 0, 0));
   pixels2.setPixelColor(i-1, pixels2.Color(255, 62.5, 0));
   pixels2.setPixelColor(i-2, pixels2.Color(255, 127.5, 0));
   pixels2.setPixelColor(i-3, pixels2.Color(0, 255, 0));
   pixels2.setPixelColor(i-4, pixels2.Color(0, 127.5, 255));
   pixels2.setPixelColor(i-5, pixels2.Color(0, 0, 255));
   pixels2.setPixelColor(i-6, pixels2.Color(255, 0, 255));
   pixels2.setPixelColor(i-7, pixels2.Color(0, 0, 0));

   pixels2.setPixelColor(i-60, pixels2.Color(125, 0, 0));
   pixels2.setPixelColor(i-61, pixels2.Color(125, 31, 0));
   pixels2.setPixelColor(i-62, pixels2.Color(125, 62, 0));
   pixels2.setPixelColor(i-63, pixels2.Color(0, 125, 0));
   pixels2.setPixelColor(i-64, pixels2.Color(0, 62, 125));
   pixels2.setPixelColor(i-65, pixels2.Color(0, 0, 125));
   pixels2.setPixelColor(i-66, pixels2.Color(125, 0, 125));
   pixels2.setPixelColor(i-67, pixels2.Color(0, 0, 0));


   pixels2.setPixelColor(i-120, pixels2.Color(125, 0, 0));
   pixels2.setPixelColor(i-121, pixels2.Color(125, 31, 0));
   pixels2.setPixelColor(i-122, pixels2.Color(125, 62, 0));
   pixels2.setPixelColor(i-123, pixels2.Color(0, 125, 0));
   pixels2.setPixelColor(i-124, pixels2.Color(0, 62, 125));
   pixels2.setPixelColor(i-125, pixels2.Color(0, 0, 125));
   pixels2.setPixelColor(i-126, pixels2.Color(125, 0, 125));
   pixels2.setPixelColor(i-127, pixels2.Color(0, 0, 0));
   
 
    
   
   pixels2.show();
   delay(DELAYVAL300*4);
    }
    
    for(int i=0; i<NUMPIXELS2; i++) {


    pixels2.setPixelColor(i, pixels2.Color(0, 0, 0));
     pixels2.show();
   
    }
     delay(BIGDELAYLOOP);
    
    
    //triple sparkle

     for (int a=0; a<100; a++)
{
long w= random(0,NUMPIXELS);
long p= random(0,NUMPIXELS);
long q= random(0,NUMPIXELS);
long ww= random(0,NUMPIXELS2);
long pp= random(0,NUMPIXELS2);
long qq= random(0,NUMPIXELS2);

    pixels.setPixelColor(w, pixels.Color(255, 255, 255));
    pixels.show();
    pixels.setPixelColor(p, pixels.Color(255, 255, 255));
    pixels.show();
    pixels.setPixelColor(q, pixels.Color(255, 255, 255));
    pixels.show();
   
    pixels2.setPixelColor(ww, pixels2.Color(255, 255, 255));
    pixels2.show();
    pixels2.setPixelColor(pp, pixels2.Color(255, 255, 255));
    pixels2.show();
    pixels2.setPixelColor(qq, pixels2.Color(255, 255, 255));
    pixels2.show();

   delay(200);

   pixels.setPixelColor(w, pixels.Color(0, 0, 0));
   pixels.setPixelColor(p, pixels.Color(0, 0, 0));
   pixels.setPixelColor(q, pixels.Color(0, 0, 0));
   pixels.show();

   pixels2.setPixelColor(ww, pixels2.Color(0, 0, 0));
   pixels2.setPixelColor(pp, pixels2.Color(0, 0, 0));
   pixels2.setPixelColor(qq, pixels2.Color(0, 0, 0));
   pixels2.show();
}
for(int i=NUMPIXELS; i>0; i--) {


    pixels.setPixelColor(i, pixels.Color(0, 0, 0));
     pixels.show();
   
    }

    for(int i=NUMPIXELS2; i>0; i--) {


    pixels2.setPixelColor(i, pixels2.Color(0, 0, 0));
     pixels2.show();
   
    }}}

For more information on the specifics of electric currents, watch the video below:

For more information on circuits, visit this link!

How Stuff Works: Circuits

And to wire your own Elegoo Mega, visit the link here:

Elegoo Mega Data Sheet (pdf)

I first wanted to say thanks to those who have taken time to read the blog, and I hope you learned a a thing or two. This will be my last 3D molecular representations blog post and in it I will go over some of my final thoughts and show off all that I have learned.

Brief Overview of Accomplishments…

The CAD side of things…

Three months ago, I started this project by learning how to use CAD software, Fusion360, to edit STL files of 3D molecular structures that were provided by the Protein Data Bank (PDB). Through this time, I learned how to use many of the more basic tools in Fusion360 such as sketch, extrude, fillet, chamfer, split face, combine, inspect, combine mesh, tesselate, and plane cut. These tools were all I needed to make the necessary edits in creating 3D molecular models. I have a more in-depth explanation for most of these tools linked so check them out if you are interested.

The 3D-Printing side of things…

The 3D-printing side of things was a more complicated matter as there seemed to be a sort of “guaranteed chance of error” with the MMU 3D-Printer. In the beginning I was making no progress because the “Wipe Tower” would not be enabled if a particular extruder was set to only be utilized for supports. After figuring out how to work around this issue another problem arose with the soluble filament. The problem here was that the PVA filament I used would constantly clog and sometimes caused a glitch where the MMU would load and unload the filament endlessly. The work around for this was simply using a different soluble filament called BVOH filament. Even with all this there were still issues that I ultimately could not completely avoid such as clogging, simple errors, and filament expiring or going bad from too much exposure to moisture. However, I did find using a filament drier was very useful in keeping filaments in good condition for longer. That idea was from Shannon and Cartland so thanks for that one!

Final Model Montage and Final Thoughts…

Here is a picture of the new and improved BCR-ABL model without all the printing errors from before. Now, I want mention that before I talked about “oh you can show different subunits using different colors.” I just want to say I thought using two colors here would look cool and I wanted to figure out the MMU printer and it does not represent multiple subunits in this case. Also, thanks to Dr. Agrawal for choosing these colors (they look like a gender reveal but otherwise its nice).

Altogether

Apart

Video of the assembly (not including the simulated imatinib or ATP).

Final Thoughts…

I hadn’t mentioned it yet but in order to avoid the “drooping” of the filament for this print. I changed the infill from 20% to 30% and changed the orientation in which the model is printed. An example is shown below.

Before

After

Once again thanks for tuning in. I had a great time with this project, and I think I learned a good bit. I think there is much more that can be done with this concept and there are plenty examples of “model molecules” that can be printed to be used as a teaching tool. I may continue this project in my own time before presenting to the Research and Creativity Day symposium in the Spring because there was more that I wished to do. My big idea for this project was to make a series of models that can explain mechanism of molecules such as hemoglobin, but I ran out of time. For example, imagine a series of models that starts with a model of hemoglobin similar to what I had done in this project but with a highlighted section (section printed in a different filament). Then next to this model was another model that is the same color as the highlighted section (for example the porphyrin rings) which shows how the interactions of the ring to hemoglobin allows interactions with oxygen or CO2. I had an idea to make a wider model stand that can occupy two models to be displayed which would facilitate this idea. Anyways, good luck to those who wish to replicate this process.

In my last post I went over how I edited my BCR-ABL model in Fusion360 but here I will discuss the printing process. I have now returned to using the multi-extruder with some new tools and settings which I will discuss later on. Spoiler alert, IT WORKED!

New Filament…

One of the things that I was unable to do at the start of this project was use soluble filament for support structures. I had originally used a PVA filament from Polymaker which has a printing temperature of 215-225°C and costed around 60$ for a 0.75kg wheel. We have since upgraded to a BVOH filament from Verbatim which has a printing temperature of 210 ± 10°C and costed upwards of 140$ for a 500g wheel. Overall, BVOH filament is far superior in all regards as it dissolves in water faster, it does not absorb humidity as fast and therefore can last longer, the possibilities of “stringiness” during printing is lower, and the extrusion can be more continuous. Now yes, it is also far more expensive, but I was completely unable to get anything to print with PVA and I made progress with BVOH. I believe this filament was much better than PVA because the printing temperature of BVOH is very similar to that of PLA meaning temperatures remain relatively constant throughout the print. This reduces the chance of “goopy” filament extrusion due to temperatures being too high and reduces the chance of filament solidification (clogging) from temperatures being too low.

Filament Dryer…

As I previously mentioned, BVOH filament does not absorb moisture as well as PVA, however soluble filaments across the board are more susceptible to going bad from sitting out compared to other filament types. This is most apparent during prints where the filaments can be sitting in open air for hours at a time. To resolve this issue, we purchased a COMGROW Filament dryer. This dryer can hold two wheels of filament at a time which can be left running during print times. An image is posted below.

Print Settings…

Now these print settings have not changed much, and the biggest difference was made by using a different filament with a filament dryer.

The main changes that I wish to highlight are all under “Options for support material and raft.”

• Style: Organic (read my last post for more details on organic supports)
• Top Contact Z distance: 0 (this is what is recommended for soluble support printing)
• Top Interface layer: 1 (this is just to further improve upon removal of supports)
• Interface pattern: concentric (this is what is recommended for soluble support printing)

These are the temperatures I had set for the PLA extruders. (note: bed temperature was later set to 70°C)

These are the temperatures I had set for the BVOH extruder. (note: bed temperature was later set to 70°C)

BCR-ABL Printed…

This will be a small montage of the print including a video of the soluble supports submerged in water. See you one last time next week!

Shows off the model fully connected together with Imatinib (red) in the substrate binding pocket.

This print was a major success however there were some issues. As you can see in the second image one of the pegs broke while I was trying to join the pieces. This issue can be solved by increasing the infill to strengthen the pegs. In the third image you can see apparent warping to the pink half. This issue is something that I don’t understand yet. I assume because the model was printed peg side down there was drooping of the model despite using supports. In the final model I hope to avoid these issues by increasing infill, printing the model flipped so the peg side is up allowing for a stronger base to avoid drooping, and increasing the bed temperatures to allow the filament to stick better.

Well, here we are. This project stared in May on a whim and prayer thanks to this one show I saw in D.C., and now I am putting together an actual project that has my face and voice behind it! I want to start this by saying a big thank you to everyone who inspired this project, funded this project, and took time to help me throughout the process of writing and filming.

The statistics are here! A whole script is here with some reflection editing to follow in January, plus a special surprise that I will later talking about. Like the script, most of the filming is done, except for that surprise I am going to mention in January. I will attach everything at the bottom of this post.

I was extremely lucky enough to interview three lovely people throughout this journey. I forgot to take pictures of these lovely people because I was so nervous, but I am so excited to share who these are with.

Lorelei d’Andriole is currently an assistant professor at Michigan State University who went to grad school at the University of Iowa, a hotspot for fluxus work. Lorelei and I spoke for way too long, and she will be heavily featured in this video essay.

Victoria Scrimer is an assistant professor at Millikin University, and probably the whole catalyst for this whole project. She worked with me through a different version of this project which was a fifteen page paper. I am so excited to show her knowledge about this subject in video form.

TG, who I want to protect for her privacy right now, is a Chicago-based part time performance artist that I met in 2022. Our interview is not the sit down typical interview, but us playing a video game where we are talking about how it feels to be alive and trans in 2024. I wanted to include someone in my life who knows my work and I know their work. TG is one of my best friends, and I cannot understate how happy I am to include them in this project.

The main film I need to get is B-roll. I need something else to be in this essay without the faces of people I know in the frame. The second thing I need to film is going to be the performance part of this piece. I feel like it would be incomplete without me doing a little performance piece based off of a fluxus score. I won’t reveal the fluxus score now, but yes, there is a performance art piece to this.

Happy 2024 wrapped.

Hey everyone, this will be a short post today with another planned to go live by the end of the week. I left off giving a sneak peek into the next modeling project I planned with BCR-ABL. This post will go over the process I went through to edit this structure in Fusion360.

Firstly, the STL files for BCR-ABL and Gleevec (Imatinib) were obtained from the link provided. Chronic myeloid leukemia (CML) is a cancer of white blood cells. In CML, white blood cells divide uncontrollably due to an overactive tyrosine kinase protein called BCR-ABL, which results from a chromosomal translocation. This chromosomal translocation creates what is known as the “Philadelphia chromosome.” Research into CML treatments has consisted of understanding the mechanisms of BCR-ABL. Since BCR-ABL is classified as a kinase enzyme there is an interaction with ATP. Researchers were able to understand that inhibition of ATP to BCR-ABL resulted in deactivation. This led to the production of Imatinib, an inhibitory drug that binds to BCR-ABL competitively with ATP.

Editing BCR-ABL in Fusion360

Since the mechanism of Imatinib binding with BCR-ABL involves a conformational change that locks the molecule inside BCR-ABL, I had to do a slightly different design for modeling the substrate binding. In this new design the model of BCR-ABL is split down the middle allowing for the model of Imatinib to be inserted in the substrate binding zone before closing the BCR-ABL model. The same process can be done with ATP to show the similar binding process.

This was completed by using the “Plane Cut” function. This can be found under the “Mesh” tab, subsection “Modify.” When using this command ensure that “Type” is set to split body and “Filly Type” is set to uniform.

Two cylindrical tubes were created at around a 50mm diameter (important for later) and positioned in areas that allow them to act as pegs when printed.

These cylindrical tubes underwent the “Tessellate” function (found in the “Mesh” tab, subsection “Create”) and subsequently the “Combine, cut” function (found in the “Mesh” tab, subsection “Modify”) was used with each half of the BCR-ABL model creating a hole for the peg (one for each half).

A new set of cylinders was created using the same process as before but at around a 48mm diameter. The diameter was reduced slightly as in the last print using pegs, I found it was too difficult to pull the model apart.

I decided to use the same stand that I created before since it looked quite nice, and I had no issues with it. The procedure for completing this process is outlined in one of my previous posts if you are interested.

This is an image of the final product. In my next post, which will go live either tonight or tomorrow tonight, I will go over the printing process for this model. The next post after that is my last post in this series 🙁 which will go over my final project in its entirety.

Over the shuffle of my birthday, Thanksgiving, and the whole world, I forgot to update with one important post. The State of the Video will be the next post directly after this. Thanks!

I just did an interview with the DKC podcast about my inspiration coming into this project, what made me nervous about this project, and what I want people to learn out of this project. I talk a lot about the past, the vanishing act of documentation about queer art, and if we should eat candy if the candy represents someone else’s lover. I have a horrible memory, so I hope you enjoy this podcast as much as I do when I relisten to my voice.

In the past few weeks, a lot of recording has happened. My script is full and my camera’s SD card might be full, so soon I will start editing. My computer setup in the corner of my apartment is full of fun little audio gadgets and editing software, so I am excited about the prospect of sitting at my desk for multiple hours and getting into this zen-like mode after classes.

I will pause for finals and other stuff. Even though I love the work of editing, the work/life balance of it all does apply to work I love.

Sadly, I do have to start this post differently than the other ones. 

This project is an inherently political project. This project stems from both love and hatred for the theatre community that built me up since age eight to ultimately reject me for who I was at twenty-three. There was a rejection for who I was in the context of politics.

Donald Trump ran a campaign based on policies to get rid of trans* people in the public eye (banning trans women from sports, stripping our history from school curriculums and libraries across the United States) and getting rid of the care we need starting from denying those under eighteen access to reversible puberty blockers and in those who are old enough to start hormone replacement therapy (or HRT), hormones. About 1.1% of Americans identify as transgender, and another 1.5% did not identify as either male or female, leading to the assumption that these individuals are nonbinary. This is the creation of a trans hysteria. 

I do not have the time to doom over the policies of our president-elect– I spent the weekend doing that already. What I do have time for is how to make this into art. The election threw in another chapter into this video essay. I am speaking with friends and former interviewees about the recent election, and that impact on their art. I will be talking to more people about how art from other times of oppression lead to the creation of today’s art.

For now, I will be rewriting bits, choosing a new center to focus on, and going through with that plan.

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.

The creative block is here.

I really talk about “blocks” in creativity when it comes to reading or writing. I cannot finish a book or I cannot finish writing a piece. Those feelings are valid and true even when you are the only one stopping yourself. The new frontier, for me, is combining both the feelings of art and research. Well, I have hit the researcher’s block.

There is a little site on the internet called the Internet Archive. I highly encourage everyone to at least see the library of what they offer. Earlier in the month, someone launched a DDOS attack on the site, making the public lose access to tons of data only found on the Internet Archive. This for me was a pinnacle moment. Libraries do not keep access to weird art, they keep access to what is most circulated and what will be most circulated. A “dead” art movement might be the first thing gone. When I saw the Internet Archive was down, I sat down with my advisors on this project and asked what I could do.

The answer? Wait.

After the month of October, I can finally log in. This was impossible yesterday when I checked on the site. The writing and recording of artists all around the globe are now back. I still wonder if I am in that creative block still. I only found out about the log in a minute ago. I still cannot explain the pouring of emotion over me. My job is back, but do I dive back in or wade in the waters?

Hello everyone, this is my fourth blog post that outlines updates on my 3D molecular representations project. This one might be shorter than previous posts, but there are a few things that I need to address. Firstly, the soluble support that I was using previously (Polydissolve S1 from Polymaker, PVA Filament) went bad and I am currently waiting for the new filament to come in. I was not aware that I needed to keep this filament in a very dry environment, and it seems the filament absorbed too much moisture and became extremely flimsy. This seems to be the reason why there were so many MMU loading errors and misprints as when the filament tries to move through the MMU tubing and into the MMU extruder it kept getting jammed. Secondly, I have tried to transition into using a combination of PETG/PLA filaments instead of the PLA/PVA filaments however I am still having issues with printing with multiple filaments.

Side note: That weird white looking stuff on the base is spray glue from when I attempted to save this print with the only glue that I had near me… 🙁

Stand Issue… And SOLUTION!

I was satisfied with the old stand design, however, when I attempted to remove the supports, the peg snapped, and I decided to redesign the stand. The issue seemed to be a lack of support to the base of the peg which made it very unstable. Also, remember in a previous post I talked about added a simple design in the stand that displays the molecular name… well I did it and it turned out quite nicely. The new design is shown below:

Also, this grey filament is PETG just like with the blue filament shown previously, and I must say it looks so much better than PLA. But just like with PLA, I still have some “support scarring” on the bottom of the model as shown below.

Different Print Settings…

I decided to make an effort to supplement the soluble support and did some digging into the advanced print settings on Prusa and found a few interesting things. Firstly, the default print settings have the interface pattern set to one that is most ideal for soluble supports and there is another setting that is recommended when soluble supports are not used.

Under the “Print Settings” tab in Prusa, there is the “Rectilinear” option, which is ideal for non-soluble supports while the “Concentric” option is for soluble supports.

Secondly, there is an option to make the interface layer between the supports and model much thinner and therefore easier to remove.

Thirdly, there are support pattern options labeled “Grid,” “Snug,” and “Organic” which essentially changes the design of the support.

• Grid: The default style that prioritizes sturdiness over all else and can result in supports that are extremely difficult to remove.
• Snug: Similar to Grid except the supports conform to the shape of overhangs and results in reducing filament waste, easier to remove supports, and reduced stability in some parts of the print.
• Organic: Think of tree branches that wrap around the model to give support instead of scaffolding like with Grid and Snug. This method is fast and cheap to print however it is a poor option for some models and often excels when used to print something like a mini figure.

In the past I have always used “Grid” as that is what is set at default however, I tried using “Snug” for the redesign stand, and I personally think it helped with support removal. I have yet to use Organic however, I will be trying that sometime this week. Below is an image of the “Organic” support style that I found on google since it can be hard to visualized.

Next Steps…

My next objective is to take a molecular structure like hemoglobin and separate it into its 4 subunits (2 alpha and 2 beta subunits) for multiple reasons:

1. This will allow for the models to be disassembled to be viewed as not just one structure but as multiple structures that come together and form one structure.
2. This will improve print quality because molecular models are very complex and the autogenerated supports within the model can get stuck. This wouldn’t be an issue if I could figure out soluble support printing, but you know how that goes.
3. This will allow for larger models to be printed as the separate parts can be arranged on the heat bed instead of altogether. This can further improve print quality as well because the model is being printed in a more horizontal fashion instead of vertically.
4. This will allow pegs to be created in locations of known cysteine-cysteine disulfide bridges to further illustrate how these amazing molecules are created and folded. This is not just for looks either as the pegs will allow the model to be put together and displayed on the stand.

That’s all for now. See you next week!