P R O T E I N V I E W Explore molecular structures in your terminal <a href="LICENSE"><img src="https://img.shields.io/badge/License-MIT-blue.svg" alt="License: MIT"></a> <a href="https://www.rust-lang.org/"><img src="https://img.shields.io/badge/Rust-1.85%2B-orange.svg" alt="Rust"></a> <img src="https://img.shields.io/badge/version-0.3.0-green.svg" alt="Version"> <a href="https://github.com/001TMF/ProteinView/pulls"><img src="https://img.shields.io/badge/PRs-welcome-brightgreen.svg" alt="PRs Welcome"></a> <a href="https://www.linkedin.com/in/tristan-farmer-973b7a17a/"><img src="https://img.shields.io/badge/LinkedIn-Tristan%20Farmer-0A66C2?logo=linkedin" alt="LinkedIn"></a> <img src="assets/hero-histone.png" alt="Nucleosome core particle with histone proteins and DNA rendered in FullHD mode" width="700"> Nucleosome core particle — histone octamer wrapped in DNA, rendered with Kitty graphics protocol

Terminal molecular structure viewer — load, rotate, and explore proteins, nucleic acids, and small molecules from PDB/CIF files right in your terminal. No browser, no GUI, no dependencies.

Features

3-tier render modes — Braille, HD, and FullHD (Sixel/Kitty) with automatic SSH detection
PNG-compressed Kitty protocol — ~10-20x smaller than raw RGBA, making FullHD viable over SSH
Cartoon ribbon visualization — Lambert-shaded ribbons with depth fog for helices, sheets, and coils
RNA/DNA support — backbone, wireframe, and cartoon modes with base-type coloring
Small molecule rendering — ligands as ball-and-stick, ions as spheres
Interface analysis — inter-chain contacts, binding pockets, and interaction visualization (H-bonds, salt bridges, hydrophobic contacts)
7 color schemes — structure, chain, element (CPK), B-factor, rainbow, pLDDT (AlphaFold)
Interactive controls — vim-style rotation, zoom, pan with auto-rotation
PDB & mmCIF — both formats supported, with RCSB PDB fetch (--fetch)
Single static binary — zero runtime dependencies

Render Modes

Three rendering tiers to match your terminal and connection:

<img src="assets/render-modes-grid.png" alt="Braille vs HD vs FullHD rendering comparison" width="700"> Left: Braille (works everywhere, including SSH/tmux) · Middle: HD (Lambert-shaded braille) · Right: FullHD (Kitty pixel graphics)

| Mode | Key | Quality | SSH Performance | |------|-----|---------|-----------------| | Braille | default | Text-based, monochrome per cell | Excellent | | HD | m | Shaded braille with lighting + depth fog | Excellent | | FullHD | M | Sixel/Kitty pixel graphics | Good (PNG compressed) |

--hd is SSH-aware: defaults to HD over SSH, FullHD locally. Use --fullhd to force pixel graphics.

Visualization Modes

<img src="assets/viz-modes-grid.png" alt="Cartoon, Wireframe, and Backbone visualization modes" width="700"> Left: Cartoon (ribbon) · Middle: Wireframe (all-atom) · Right: Backbone (CA trace)

| Mode | Description | |------|-------------| | Cartoon | Smooth ribbon rendering — helices, beta-sheets, and coils with Lambert shading. Default. | | Wireframe | All-atom bonds including inter-residue peptide and phosphodiester linkages. | | Backbone | CA trace (proteins) / C4' trace (nucleic acids) with spheres and thick connecting lines. |

Interface Analysis & Interactions

<img src="assets/interface-grid.png" alt="Interface analysis with interaction visualization" width="700"> Left: Interface residue coloring with sidebar panel · Right: Dashed interaction lines (H-bonds, salt bridges, hydrophobic contacts)

Press f to toggle interface mode — highlights contact residues across chain boundaries with a detailed sidebar. Press I to overlay interaction lines:

| Color | Interaction | Distance | |-------|-------------|----------| | Cyan | Hydrogen bond | ≤ 3.5 Å | | Red | Salt bridge | ≤ 4.0 Å | | Yellow | Hydrophobic contact | ≤ 4.5 Å | | Gray | Other | ≤ 4.5 Å |

Nucleic Acids

<img src="assets/dna-element.png" alt="B-DNA double helix with element (CPK) coloring" width="500"> B-DNA dodecamer in wireframe mode with CPK element coloring

Full support for DNA and RNA structures — backbone traces, wireframe bonds, and cartoon ribbons with nucleotide base-type coloring (A=red, U/T=blue, G=green, C=yellow).

AlphaFold & pLDDT

<img src="assets/plddt-cartoon.png" alt="AlphaFold prediction with pLDDT confidence coloring" width="500"> AlphaFold prediction with pLDDT confidence coloring — blue (high confidence) to orange/yellow (low confidence)

Automatically detects AlphaFold structures and offers pLDDT confidence coloring. Cycle through color schemes with c.

Installation

Requires Rust 1.85+. If you don't have Rust, install it with:

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

Then install proteinview:

git clone https://github.com/001TMF/ProteinView.git
cd ProteinView

# Basic install
cargo install --path .

# With RCSB PDB fetch support
cargo install --path . --features fetch

# Update an existing installation
cargo install --path . --force

Quick Start

# View a local PDB file
proteinview examples/1AOI.pdb

# HD mode (fast text-based shading)
proteinview examples/4HHB.pdb --hd

# FullHD pixel mode (Kitty/Sixel terminals)
proteinview examples/4HHB.pdb --fullhd

# Fetch from RCSB PDB
proteinview --fetch 1UBQ

# Choose color scheme and visualization
proteinview examples/1UBQ.pdb --color rainbow --mode wireframe

Keybindings

| Key | Action | |-----|--------| | h/l | Rotate Y | | j/k | Rotate X | | u/i | Roll | | +/- | Zoom | | w/a/s/d | Pan | | r | Reset view | | c | Cycle color scheme | | v | Cycle viz mode | | m | Braille / HD | | M | HD / FullHD | | f | Interface analysis | | I | Interface interactions | | g | Toggle ligands | | [/] | Prev/next chain | | Space | Auto-rotate | | ? | Help | | q | Quit |

Color Schemes

| Scheme | Description | |--------|-------------| | Structure | Helix (red), sheet (yellow), coil (green). Default. | | Chain | Distinct color per chain. | | Element | CPK coloring (C, N, O, S, P, metals). | | B-factor | Blue (rigid) to red (flexible). | | Rainbow | N-terminus (blue) to C-terminus (red). | | pLDDT | AlphaFold confidence (blue=high, orange=low). |

Terminal Support

| Terminal | Braille | HD | FullHD | |----------|---------|-----|--------| | Any Unicode terminal | Yes | Yes | -- | | Kitty | Yes | Yes | Yes (PNG) | | WezTerm | Yes | Yes | Yes (Sixel) | | iTerm2 | Yes | Yes | Yes | | foot | Yes | Yes | Yes (Sixel) | | tmux/screen | Yes | Yes | -- |

Building

cargo build --release

# With RCSB fetch support
cargo build --release --features fetch

Contributing

Contributions are welcome! Here's how to get started:

Fork the repository
Create a feature branch (git checkout -b feature/my-feature)
Make your changes and add tests
Run cargo test to verify
Open a pull request against develop

Please open an issue first for major changes to discuss the approach.

License

MIT

ProteinView

Install / Use

README