Servalcat - refinement and map calculation

Servalcat (for Structure refinement and validation for crystallography and single particle analysis) is a software package for atomic model refinement and map calculation.

Source code repository: https://github.com/keitaroyam/servalcat

Installation

Please see https://github.com/keitaroyam/servalcat/blob/main/README.md#installation

References

Cryo-EM SPA refinement:

Yamashita, K., Palmer, C. M., Burnley, T., Murshudov, G. N. (2021) “Cryo-EM single particle structure refinement and map calculation using Servalcat” Acta Cryst. D77, 1282-1291

Refmacat and restraint generation using GEMMI:

Yamashita, K., Wojdyr, M., Long, F., Nicholls, R. A., Murshudov, G. N. (2023) “GEMMI and Servalcat restrain REFMAC5” Acta Cryst. D79, 368-373

Table of Contents

• Overview
  • Command examples for cryo-EM SPA
  • Command examples for crystallography
• Single particle analysis (SPA)
  • Half maps
  • Point group symmetry
  • Helical symmetry
• SPA examples
  • Refinement of ChRmine structure
  • Refinement of amyloid-β 42 structure
  • Calculating Fo-Fc omit map
• Crystallographic refinement
  • Getting started
  • Frequently used options
  • Input columns for diffraction data
  • Logs and statistics
  • Radiation sources
  • Small molecules
  • Complete list of options
• Supported Refmac keywords
  • External restraints
  • Restraint weights
  • Controlling restraints
• Scattering source
  • X-ray
  • Electron
  • Neutron
  • Custom
• Handling hydrogen atoms
  • Control keywords
  • Generating all hydrogen atoms explicitly
  • Tautomers and protonation states
• Servalcat commands
  • SPA
  • Utilities