servalcat - Cryo-EM SPA Reciprocal-Space Refinement Tool
Performs reciprocal-space refinement and map calculation for cryo-EM SPA and crystallography
Tags
Updated: 2026-05-09Capabilities
Typical Inputs
Typical Outputs
What this skill does
- refine models against half-maps
- calculate Fo-Fc maps
- calculate omit maps
- trim map files
- expand NCS symmetry
- find map peaks
- convert FSC JSON to CSV
- refine crystallographic models
Inputs
- PDB model file
- mmCIF model file
- half-map files
- resolution value
- mask file
- ligand restraint dictionary
- point group symmetry
- helical symmetry parameters
- keyword restraint file
Outputs
- refined PDB model
- refined mmCIF model
- symmetry-expanded model
- Fo-Fc map files
- normalized Fo-Fc map
- FSC curve log
- Coot script
Requirements
- unsharpened half-maps
- Python environment
- pip or CCP4 v9.0+