Structure refinement and validation for crystallography and single particle analysis

Project description

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.

Installing the lastest (unstable) version

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

Usage

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

References

Project details

Release history Release notifications | RSS feed

This version

0.4.142

Jun 21, 2026

0.4.131

Feb 2, 2026

0.4.128

Jan 2, 2026

0.4.126

Dec 16, 2025

0.4.118

Sep 2, 2025

0.4.105

Apr 1, 2025

0.4.100

Feb 20, 2025

0.4.99

Dec 11, 2024

0.4.88

Sep 14, 2024

0.4.72

Jun 12, 2024

0.4.60

Mar 11, 2024

0.4.39

Nov 2, 2023

0.4.32

Aug 9, 2023

0.4.24

May 31, 2023

0.4.15

Apr 20, 2023

0.4.0

Mar 7, 2023

0.3.0

Dec 31, 2022

0.2.122

Sep 27, 2022

0.2.116

Aug 19, 2022

0.2.95

Apr 25, 2022

0.2.62

Mar 17, 2022

0.2.23

Dec 10, 2021

0.2.0

Sep 28, 2021

0.1.0

May 26, 2021

0.0.1

Feb 16, 2021

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servalcat 0.4.142

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