MolX

MolX is an interactive protein-structure viewer for graphical terminals. It opens PDB files, renders a smooth protein ribbon as a high-resolution raster, and lets you rotate and zoom without leaving the command line. It also connects to the ESM Metagenomic Atlas to fetch existing predictions, display predicted aligned error (PAE), or fold a short amino-acid sequence with the public ESMFold service.

The viewer uses the repository's rstui runtime and automatically selects Kitty graphics, iTerm2 images, Sixel, or an ANSI truecolor fallback.

Build and run

cd molx
cargo run --release -- view protein.pdb

Install the molx command from this checkout:

cargo install --path molx
molx view protein.pdb

PDB viewer

molx view protein.pdb
molx view protein.pdb --representation ribbon
molx view protein.pdb --representation atoms --color element
molx view prediction.pdb --representation combined --color confidence
molx info protein.pdb
molx snapshot protein.pdb --output protein.png

MolX reads the first model in a PDB file, keeps the primary alternate location, shows ATOM and HETATM records, and constructs a gap-aware ribbon/cartoon from the protein backbone. The ribbon uses backbone torsion angles to recognize alpha helices and beta strands, smooths the path between C-alpha atoms, and adds arrowheads to beta strands. Available representations are ribbon, atoms, and combined; backbone remains accepted as an alias for ribbon.

Controls:

• Drag with the left mouse button, or use arrow keys / h, j, k, l, to rotate.
• Use the mouse wheel or + / - to zoom.
• Press m to cycle molecular representations.
• Press c to cycle chain, element, and pLDDT/B-factor colors.
• Press Space to toggle automatic rotation.
• Press r to reset the camera and q or Escape to quit.

For ESMFold structures, --color auto selects the pLDDT palette used by the Atlas: blue is high confidence and red is low confidence.

ESM Atlas

Download an existing prediction by MGnify protein identifier:

molx atlas fetch MGYP002537940442
molx atlas fetch MGYP002537940442 --output example.pdb --view
molx snapshot example.pdb --atlas-id MGYP002537940442 --output atlas.png

Fold one sequence using the public ESMFold endpoint:

molx atlas fold --sequence MKTAYIAKQRQISFVKSHFSRQ --output folded.pdb --view
molx atlas fold --fasta protein.fasta --output folded.pdb

Existing output files are preserved unless --force is passed. The public API is rate-limited and intended for a small number of interactive predictions, not bulk folding. MolX limits requests to 1,024 residues and uses a five-minute request timeout. The Atlas data is distributed under CC BY 4.0; retain the appropriate attribution when redistributing downloaded structures.

atlas fetch --view retrieves the entry's PAE matrix and displays it in a right-hand heatmap next to the 3D ribbon. The live atlas fold endpoint returns a PDB prediction but no PAE matrix, so its viewer panel reports PAE as unavailable.

Official resources:

• https://esmatlas.com/about#api
• https://github.com/facebookresearch/esm

Current scope

This first version focuses on local PDB viewing and stable public ESM Atlas operations. mmCIF parsing, residue selection, surfaces, ligand bond inference, measurements, and sequence/structure search are natural next modules.