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

See Your First Structure#

  1. Navigate to any GitHub or GitLab repository that contains a .pdb, .cif, or other supported file
  2. Look for a green Mol (MVS)* badge next to file names in the file browser, or next to links in README files
  3. 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):

  1. Click the Mol* Linker extension icon in your browser toolbar.
  2. Drag and Drop your local `.pdb`, `.cif`, or `.gro` file directly into the dashed box.
  3. The workspace will instantly open and render your file locally—no upload required!

Change the Active Preset#

Click the extension icon in your browser toolbar to open the popup:

  1. Select a preset from the Active Configuration dropdown (e.g. “Protein Surface + Spacefill Ligands”)
  2. Click Apply & Reload Tab
  3. The current page reloads and new badges will use the selected preset

Open the Full Settings Studio#

Click Open Advanced Studio in the popup, or right-click the extension icon and choose Options. The studio lets you configure representations, colors, custom highlight rules, and templates in detail — see Configuration.

Working with Unknown Databases#

Mol* Linker is equipped with a Universal “Smart Scanner” that can automatically detect structural files on almost any database (like Figshare, Zenodo, or university servers). If the extension detects a valid structure nearby, the Mol* Workspace badge will appear automatically.

The Right-Click Fallback & Gatekeeper#

If you are on a highly customized database (like Figshare or Zenodo) where the green badge does not automatically appear next to a download link:

  1. Right-Click the download button or link.
  2. Select *“Open in Mol Workspace”** from the browser’s context menu.
  3. The Gatekeeper: If the site is not yet authorized, the extension will securely intercept the request and ask if you want to grant it access.
  4. Format Check: If the extension cannot guess the file type from the website’s code, it will present a clean dropdown asking you to confirm the format before launching.
Backward Installation Configuration & Studio Forward