Installing Molass GUI (Windows)

This page is for beginners with no Python experience. If you already have Python installed and are comfortable with pip, see the Developer install section at the bottom instead — it’s simpler for that audience.

Download

  1. Go to the Releases page.
  2. Under the latest release, download the file named molass-gui-<version>-portable-win64.zip.

  3. Right-click the downloaded zip → Extract All… and choose a folder you can find easily (e.g. your Desktop or Documents). Do not try to run the program directly from inside the zip file — it must be extracted first.

    This step can take a few minutes. The zip contains several thousand small files (the Python runtime and all of Molass’s dependencies), and Windows’ built-in “Extract All” — like most antivirus-scanned extractors — is noticeably slower on many-small-files archives than on a single large file. This is normal; it is not stuck.

No installer runs, nothing is written outside the folder you extracted to, and no administrator rights are needed — the whole program, including its own copy of Python, lives inside that one folder.

Run it

Open the extracted folder and double-click molass-gui.bat.

A window titled Molass should appear after a few seconds. If a security warning appears first, see Windows SmartScreen warning below.

Try it with sample data

The GUI needs a folder of SEC-SAXS data to analyze. If you don’t have your own data yet, Molass ships with public sample datasets for exactly this purpose — see the Quick Start guide, which walks through a complete analysis using one of them (SAMPLE1), with screenshots of every step.

Troubleshooting

Windows SmartScreen warning

Because this build isn’t digitally signed by a registered publisher, Windows may show a blue “Windows protected your PC” screen the first time you run molass-gui.bat. Click More info, then Run anyway. This is expected for small open-source projects distributed outside the Microsoft Store and does not indicate a problem with the download.

Antivirus flags the extraction or the folder

Some antivirus products scan every file during a large extraction, which can make it feel stuck — give it a few minutes before assuming something is wrong. If your antivirus quarantines a specific file afterward, it is almost always a false positive on one of the bundled scientific-Python native libraries (e.g. numba/llvmlite); restoring it from quarantine is safe.

The window never appears / closes immediately

Make sure you extracted the whole zip (not just opened it) and are running molass-gui.bat from inside the extracted folder, not from inside the zip itself (Windows lets you browse into a zip without extracting it, but programs can’t run correctly from there).

If it still doesn’t work, please open an issue — include what you see (or a screenshot) and your Windows version.

Developer install (pip)

If you already have Python 3.9–3.14 installed:

pip install molass-gui
molass-gui

See the repository README for details and version requirements. This route also works on macOS/Linux, unlike the portable zip above, which is Windows-only.