Mol* Linker on Mol* Linker Wiki

Scene Settings

Mon, 01 Jan 0001 00:00:00 +0000

The Global Scene Settings panel controls the overall look of the Mol* viewer, independent of any particular molecule.

Canvas Background Color#

Sets the viewer background. Click the color swatch to open a color picker, or type a hex value directly (e.g. #111111 for dark mode).

The default is white (#ffffff). If you want a dark background without changing anything else, use the built-in Dark Mode Canvas preset from the popup.

Molecular Targets

Mon, 01 Jan 0001 00:00:00 +0000

The Global Target Configurations panel lets you set the default visual style for each class of molecule. Each target is a collapsible card.

Available Targets#

Target	Selector	Default Representation	Default Color
Proteins	`protein`	Cartoon	Chain ID
Nucleic Acids (DNA/RNA)	`nucleic`	Cartoon	Chain ID
Ligands & Small Molecules	`ligand`	Ball & Stick	Element symbol
Carbohydrates & Glycans	`branched`	Ball & Stick	Element symbol
Lipids	`lipid`	Ball & Stick	Element symbol
Single Ions	`ion`	Ball & Stick	Element symbol
Water / Solvent	`water`	Hidden (Off)	—
All Atoms	`all`	Ball & Stick	Element symbol

The all target is a catch-all that applies to every atom in the structure. It is useful as a fallback representation but is hidden by default. Enable it only when you want a uniform style applied across the entire structure regardless of molecule type.

Custom Rules

Mon, 01 Jan 0001 00:00:00 +0000

Custom rules let you target specific chains, residues, or atoms and apply a color override or a completely separate representation on top of (or instead of) the global target settings.

Click + Add New Rule at the bottom of the Custom Highlighting Rules panel to create one.

Rule Types#

Highlight (color overlay)#

Overlays a color on the existing representation without adding new geometry. Use this to call attention to a residue range or chain while keeping the surrounding context intact.

Architecture & Execution Flow

Mon, 01 Jan 0001 00:00:00 +0000

Core Philosophy#

Mol* Linker operates across several strict security boundaries imposed by the browser. Modern browsers enforce Content Security Policies (CSP) that block unsafe-eval in Manifest V3 extension pages, and restrict cross-origin requests (CORS) between websites and external servers.

To load multi-megabyte structural files from dynamic Single Page Applications (GitHub, GitLab, RCSB) into a high-performance WebGL visualizer (Mol*), the extension uses a 4-Layer Architecture where each layer has one clearly defined responsibility.

Contributing & Build System

Mon, 01 Jan 0001 00:00:00 +0000

Development Workflow#

Mol* Linker is written in TypeScript and uses a two-stage build pipeline:

Type checking — tsc --noEmit validates the entire codebase against strict TypeScript rules without producing any output files.
Bundling — esbuild takes each entry-point module and bundles it with all its dependencies into a single, self-contained JavaScript file per page.
Assembly — assemble.js copies the bundled JS, static HTML/CSS, icons, and the correct browser manifest into a browser-specific output folder.

This separation means the TypeScript compiler is a pure quality gate, and esbuild handles the actual output — giving you both type safety and fast, modern output with zero runtime overhead.

Frequently Asked Questions

Mon, 01 Jan 0001 00:00:00 +0000

General Questions#

Where did my data go? Does this extension upload my proprietary files?#

Absolutely not. This is one of the biggest upgrades in Mol* Linker v2.0. Older versions of this tool (and many other visualizers) had to redirect you to external servers. Mol* Linker now opens a dedicated, local workspace directly inside your browser.

When you click a badge, the extension securely downloads the file straight into your browser’s active, temporary memory (RAM). It never touches your hard drive, and it is never uploaded or sent to any external visualization servers. The moment you close the tab, the data ceases to exist. It is 100% private.

Installation

Mon, 01 Jan 0001 00:00:00 +0000

Official Web Stores#

The easiest and safest way to install Mol* Linker is through the official browser extension stores. These versions update automatically and have passed rigorous security reviews.

Install for Google Chrome / Edge / Brave (Coming Soon)
Install for Mozilla Firefox (Coming Soon)

Manual Installation (Developers & Advanced Users)#

If you want to test the latest features before they hit the web store, or if you want to modify the source code, you can install the extension manually.

Module Reference

Mon, 01 Jan 0001 00:00:00 +0000

All source files live in src/ and are written in TypeScript. Each entry-point module is compiled by esbuild into a single self-contained .js file in dist/. Shared modules (types, config, permissions, mvs-builder) are not separate output files — they are bundled into whichever entry points import them.

Shared Modules#

`src/types.ts`#

Defines all shared TypeScript interfaces and the inter-context message protocol. This is the single source of truth for data shapes across the entire codebase.

Quickstart

Mon, 01 Jan 0001 00:00:00 +0000

Once the extension is installed, no configuration is needed to get started.

See Your First Structure#

Navigate to any GitHub or GitLab repository that contains a .pdb, .cif, or other supported file
Look for a green Mol (MVS)* badge next to file names in the file browser, or next to links in README files
Click the badge — the structure opens in the Mol* viewer in a new tab, rendered with your current settings

View Local Files (Drag & Drop)#

Mol* Linker doubles as a lightning-fast offline desktop viewer! If you have a structure on your computer (e.g., from AlphaFold or PyMOL):

Security

Mon, 01 Jan 0001 00:00:00 +0000

Security & Threat Mitigation#

Browser extensions that handle cross-origin data and execute complex rendering engines are frequent targets for security audits. Mol* Linker employs a strict Defense-in-Depth strategy to protect user privacy, prevent malicious payload execution, and secure local networks.

Here is a breakdown of the active security layers within the extension.

1. Zero-Upload Data Privacy#

The most significant security feature of Mol* Linker is its local-only architecture. When a user visualizes a proprietary, unreleased structure from a private GitLab or ElabFTW instance, the file is never uploaded to an external server. - Data is fetched directly from the authenticated host server into the browser’s volatile memory (RAM).

Mol* Linker on Mol* Linker Wiki

Scene Settings

Canvas Background Color#

Molecular Targets

Available Targets#

Custom Rules

Rule Types#

Highlight (color overlay)#

Architecture & Execution Flow

Core Philosophy#

Contributing & Build System

Development Workflow#

Frequently Asked Questions

General Questions#

Where did my data go? Does this extension upload my proprietary files?#

Installation

Official Web Stores#

Manual Installation (Developers & Advanced Users)#

Module Reference

Shared Modules#

src/types.ts#

Quickstart

See Your First Structure#

View Local Files (Drag & Drop)#

Security

Security & Threat Mitigation#

1. Zero-Upload Data Privacy#

`src/types.ts`#