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.

# PyPI
pip install servalcat

# Conda
conda install conda-forge::servalcat

will install the stable version.

Starting from ver. 0.4.146, a pre-release version of GEMMI is bundled with Servalcat by default. The current version in use is 0.7.6-dev (v0.7.5-178-g0d90cc10).

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.

1. Go to https://github.com/keitaroyam/servalcat/actions/workflows/ci.yml and click on the latest (top) one
2. Download "wheels2" from the Artifacts section (note: a GitHub account is required)
3. Unzip the file and provide the path to the directory using the --find-links option: python -mpip install -U --find-links=wheels2 servalcat

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

• 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