Minecraft Protein Structure import
(Dresden Science Night 2025)

This repository outlines the process of importing protein pdb structures into Minecraft

Requirements

For now we need a paid Minecraft / Mojang account.

Installing Minecraft and required Mods

Minecraft

On Arch-Linux there are a few problems with running the yay repo version of the minecraft-launcher. Therefore, we are using flatpak, which isolates the needed dependencies and gives us a easy to use installer.

flatpak install flathub com.mojang.Minecraft
flatpak run com.mojang.Minecraft

This will install minecraft to this directory: ~/.var/app/com.mojang.Minecraft/.minecraft/

Now start the minecraft-launcher and see that everything has worked (this step is mandatory). You will also be prompted to login with your minecraft account.

Forge

This is a very common mod-loader for minecraft and can be easily installed using its java installer. If the installer does not find the minecraft installation automatically, you'll need to pass the path to .minecraft (see above) manually.
We are running on Minecraft version 1.12.2. Download the corresponding Forge installer:
https://files.minecraftforge.net/net/minecraftforge/forge/index_1.12.2.html
(or use the .jar provided in the forge directory)

Now start the minecraft-launcher once until you are in the main menu of the game. Make sure to select the correct minecraft installation (Forge...) before pressing Play in the launcher

Mods

There are multiple mods you'll need to download and install now. Just download all of them into .minecraft/mods https://www.curseforge.com/minecraft/mc-mods/creativecore
https://www.curseforge.com/minecraft/mc-mods/littletiles
https://www.curseforge.com/minecraft/mc-mods/littletiles-3d-importer-exporter
(I also added a copy of the mod files in the mods directory)

Make sure you are downloading the mod for the correct Minecraft version (1.12.2)

Now you should be able to relaunch the game and use the mods!

Importing Models

The mod supports .obj and .mtl files (even .jpg textures). Because of the way we installed Minecraft, these files need to be stored inside the .minecraft folder.

The GitHub page of the mod describes how importing models works in-game:
https://github.com/Timardo/LT-3D-Importer-Exporter/wiki

Creating Protein Models

Setting up Conda

We programmatically create .obj and .mtl files from .pdb files in the pdb_2_obj.py python script. For this we first need to setup the conda environment the script runs in:

Creating Conda environment

conda create --prefix ./pymol_env

Updating environment (only use once after changing dependencies in environment.yml)

conda env update --prefix ./pymol_env

Running the script

For now all our script does is to load all .pdb files from the proteins directory and converting them to .obj and .mtl files, coloring each chain of our protein in a different color.
For our purposes, .obj files store the geometry of our proteins and where each color should be applied, while the .mtl files store color information.

conda run --prefix ./pymol_env python pdb_2_obj.py

We can also do this process manually in pymol (just without the .mtl file, see https://pymolwiki.org/index.php/Save).
Starting PyMol:

conda run --prefix ./pymol_env python -m pymol

LNoS World Download

Click here!

Bugs & Fixes

Minecraft Launcher crashes on startup on Arch-Linux

• fix: close the window, then go to .minecraft folder and delete webcache2 directory
• restart the launcher
• really annyoing, has to be done after every restart for me

BlockPrintr doesn't show some models

• this occurs because of cashing issues in the mod (I think...)
• fix: delete all folders used by BlockPrintr except the input folder. They can be found in your .minecraft/config/blockprintr