Servalcat

Structure refinement and validation for crystallography and single particle analysis

Servalcat implements pipelines that use Refmac5:

• servalcat refine_spa: cryo-EM SPA refinement pipeline
• servalcat refine_cx: small molecule crystallography

and a Refmac5 controller

• refmacat: behaves as Refmac, but uses GEMMI for restraint generation instead of MAKECIF

Now “No Refmac5” refinement programs have been actively developed:

• servalcat refine_geom: geometry optimization
• servalcat refine_spa_norefmac: "No Refmac" version of refine_spa
• servalcat refine_xtal_norefmac: crystallographic refinement

Also, it has several utility commands: servalcat util.

Installation

# PyPI
pip install servalcat

# Conda
conda install conda-forge::servalcat

will install the stable version.

The required GEMMI version is now v0.7.5. It may not work with the latest gemmi code from the github. The policy is in the main branch I only push the code that works with the latest package of GEMMI.

To use the Refmac5 related commands, you also need to install CCP4. For "No Refmac5" commands, you may just need the monomer library if CCP4 is not installed.

Notice: From ver. 0.4.6, Servalcat is no longer python-only package and has some C++ code. If you build Servalcat by yourself, probably you also need to build GEMMI using the same compiler.

Usage

Please read the documentation: https://servalcat.readthedocs.io/en/latest/

References

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