SAXSMART: SAXS Modelling and Refinement Toolkit

Overview

SAXSMART is an interactive web application for the analysis and refinement of Small-Angle X-ray Scattering (SAXS) data. It provides a user-friendly interface to perform common SAXS analyses and refine structural models against experimental data using PEPSI-SAXS.

Features

• Data Upload: Upload SAXS curves (.dat), protein sequences (.fasta), and structures (.pdb/.cif).
• Database Fetch: Fetch structural models directly from the PDB or AlphaFold Database.
• Automated Analysis: Automatic calculation of Guinier fit, P(r) distribution, and Kratky plots.
• Interactive Refinement: Integrated PEPSI-SAXS for rigid-body and flexible model refinement.
• Rich Visualization: Interactive plots and 3D molecular viewers.

Installation

From Pypi

# Create and activate a virtual environment (or use conda)
python3 -m venv .venv
source .venv/bin/activate

# Install
pip install -e saxsmart

From source

# Clone your repository
git clone https://gitlab.esrf.fr/hayden5a/saxsmart.git
cd saxsmart

# Create and activate a virtual environment (or use conda)
python3 -m venv .venv
source .venv/bin/activate

# Install
python -m pip install -U pip
pip install -e .

Note: Dependencies are declared in pyproject.toml.

Running

After installation, use the console script:

saxsmart

Alternative entry points:

python -m saxsmart

• Dash automatically serves files in the packaged assets/ directory.
• Example data is bundled under saxsmart/example_data/.

Configuration

You can configure paths via environment variables:

• PEPSI_SAXS_BIN — Full path to the pepsi-SAXS executable (if not on PATH).

  export PEPSI_SAXS_BIN=/opt/pepsi/pepsi-SAXS
  

• SAXSMART_CACHE_DIR — Override the directory for long-callback caching.

  export SAXSMART_CACHE_DIR=/scratch/$USER/saxsmart-cache
  

• SAXSMART_TEMP — Override the temporary working directory.

  export SAXSMART_TEMP=/scratch/$USER/saxsmart-tmp
  

If PEPSI-SAXS is not required for your workflow, related actions will be disabled or produce a friendly error message.

License

MIT (see LICENSE).