pdb_mod

Drop a .pdb / .ent structure file into a folder and build it in your world, block by block, atom by atom.

pdb_mod reads real Protein Data Bank files and voxelizes them into a space-filling (CPK-style) model made of colored wool — then lets you preview, move, and rotate the structure before placing it, Litematica-style. It also detects internal cavities (binding pockets) using a classic grid-based algorithm and marks them separately.

This is a visualization / education tool for looking at real molecular structures at a 1-block-per-voxel scale, not a chemistry simulator.

Features

• Real PDB parsing — reads ATOM/HETATM records (coordinates, element) from standard .pdb/.ent files.
• Space-filling model — each atom is expanded to its van der Waals radius and voxelized at 0.5 Å resolution, so the final shape reflects the molecule's actual volume, not just its backbone.
• Standard CPK coloring — element colors follow the standard Jmol/CPK reference palette, mapped to the closest of Minecraft's 16 wool colors (H=white, C=light gray, N=blue, O=red, S=yellow, P=orange, halogens=lime, etc.).
• Pocket / cavity detection — a LIGSITE-style algorithm (Hendlich, Rippmann & Barnickel, 1997) scans the empty voxels around the structure and flags enclosed cavities, rendered as light-blue stained glass so you can see where a ligand-binding pocket might be.
• Litematica-style placement — spawning a molecule opens a movable/rotatable preview (shown as a particle wireframe) before you commit any blocks:
  • Arrow keys — move the structure (X/Z)
  • Page Up / Page Down — move up/down
  • R — rotate 90°
  • Enter — confirm and place
  • Backspace — cancel
  • In-game file picker — a scrollable GUI list of every .pdb/.ent file in your folder.
  • No hard atom cap — large structures (full proteins, multi-chain assemblies) are voxelized in full; very large files will take longer and place more blocks.

Usage

1. Launch the game once so the mod creates its folder: .minecraft/pdbmod/
2. Drop any .pdb / .ent file in there (e.g. from RCSB PDB).
3. Open the picker in-game, pick a file, hit Spawn.
4. Move/rotate the preview into position, then confirm to place.

Keybinds (rebindable in Controls)

Commands

• /pdb scan — rescan the folder for files
• /pdb list — list available files
• /pdb open — open the picker GUI
• /pdb spawn <name> — start a preview for a specific file
• /pdb folder — print the folder path

Notes & limitations

• Client-side only — no server installation needed, safe for singleplayer and any server that allows client-side mods.
• 16 wool colors can't distinguish every element 1:1 — some less-common atoms share a color (documented in the source).
• Pocket detection is a simple grid-morphology heuristic, not a validated druggability tool — it doesn't distinguish surface-accessible pockets from fully buried cavities, and won't rank or score them the way fpocket/CASTp do. Treat it as "here's a plausible cavity," not a docking prediction.
• Very large structures (thousands+ atoms) can take a noticeable moment to voxelize and place.

Requirements

• Minecraft 1.21.11
• Fabric Loader ≥ 0.18.1
• Fabric API
• Java 21+