edref 3.7.3

Electron Diffraction Refinement Engine - SHELXL-compatible crystallographic refinement for 3D ED/microED

EDref

Electron Diffraction Refinement - SHELXL-compatible least-squares refinement with dynamical scattering correction for 3D ED data.

Installation

pip install edref

Quick Start

# Basic refinement
edref structure.ins --edref

# With dynamical correction (recommended for ED data)
edref structure.ins --edref --dyn-power

# Anisotropic with dynamical correction
edref structure.ins --edref --dyn-power --aniso

Dynamical Scattering Correction

EDref can correct for dynamical scattering effects that cause systematic intensity errors in electron diffraction data:

# Power-shape model (recommended)
edref structure.ins --edref --dyn-power

# With fixed parameters (no auto-optimization)
edref structure.ins --edref --dyn-power-params 0.8 0.3

Available models:

Flag	Parameters	Description
--dyn-power	α, γ	Power-shape correction (recommended)
--dyn-exp	α, d_decay	Exponential decay
--dyn-abs	α, d_half, γ	Absolute intensity model
--dynamical1	κ	Simple 1-parameter

Auto-Dyn Workflow

Automated refinement with cascading outlier removal:

# Auto-dyn with dynamical correction
edref structure.ins --auto-dyn --dyn-power

# With anisotropic refinement and weight optimization
edref structure.ins --auto-dyn --dyn-power --aniso --refine-weights

The auto-dyn workflow:

1. Initial refinement (50 cycles)
2. Cascading Z-threshold outlier removal (Z=8, 6, 4)
3. Re-refinement after each omit round

Common Options

# Resolution limits (d_max to d_min in Angstrom)
edref structure.ins --edref --resolution 20 0.8

# Number of refinement cycles
edref structure.ins --edref --cycles 100

# Extinction correction
edref structure.ins --edref --exti

# R-free cross-validation
edref structure.ins --edref --rfree

# Custom output path
edref structure.ins --edref --output refined/mystructure

Iterative Outlier Removal

For manual control over outlier removal:

edref structure.ins --edref --dyn-power --iterative \
    --iter-threshold 4 \
    --iter-rounds 10

Output Files

EDref generates:

• structure_edref.res - Refined structure (SHELXL format)
• structure_edref.fcf - Structure factors (Olex2-compatible)
• structure_corrected.hkl - Dynamically-corrected intensities
• structure_edref_refine.png - Refinement diagnostics
• structure_edref_outliers.png - Outlier analysis

SHELXL Comparison

# Run SHELXL only
edref structure.ins --shelxl

# Compare EDref vs SHELXL
edref structure.ins --compare

Key Features

• Dynamical correction - Multiple models for ED intensity correction
• Auto-dyn workflow - Automated outlier removal with cascading thresholds
• SHELXL-compatible - Reads/writes standard .ins/.res/.hkl/.fcf files
• Olex2-compatible - FCF output works directly in Olex2
• R-free validation - Cross-validation to detect overfitting
• Anisotropic ADPs - Full anisotropic refinement support
• Special positions - Automatic constraint detection

Requirements

• Python >= 3.10
• NumPy, SciPy, Matplotlib

Documentation

• Full Manual - Complete reference
• GitLab Repository

License

MIT License