Servalcat
Structure refinement and validation for crystallography and single particle analysis
Servalcat implements pipelines that use Refmac5:
servalcat refine_spa: cryo-EM SPA refinement pipelineservalcat 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 optimizationservalcat refine_spa_norefmac: "No Refmac" version of refine_spaservalcat 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-linksoption:python -mpip install -U --find-links=wheels2 servalcat
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
1 maintainer
Metadata
1 maintainer
Release files for servalcat 0.4.142
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| servalcat-0.4.142.tar.gz | 2.6 MB | Details |
Built distributions (wheels)
Total release size: 27.1 MB
Release files / servalcat-0.4.142.tar.gz
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| Tags | Source |
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Release files / servalcat-0.4.142-cp314-cp314t-win_amd64.whl
| Download URL | servalcat-0.4.142-cp314-cp314t-win_amd64.whl |
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| Size | 917.0 kB |
| Tags | CPython 3.14 CPython 3.14 free-threading Windows x86-64 |
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Release files / servalcat-0.4.142-cp314-cp314t-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
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Release files / servalcat-0.4.142-cp314-cp314t-macosx_11_0_arm64.whl
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Release files / servalcat-0.4.142-cp314-cp314t-macosx_10_15_x86_64.whl
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Release files / servalcat-0.4.142-cp314-cp314-win_amd64.whl
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Release files / servalcat-0.4.142-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
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Release files / servalcat-0.4.142-cp312-cp312-win_amd64.whl
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
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Release files / servalcat-0.4.142-cp39-cp39-win_amd64.whl
| Download URL | servalcat-0.4.142-cp39-cp39-win_amd64.whl |
|---|---|
| Size | 873.0 kB |
| Tags | CPython 3.9 Windows x86-64 |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
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Release files / servalcat-0.4.142-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
| Download URL | servalcat-0.4.142-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl |
|---|---|
| Size | 876.2 kB |
| Tags | CPython 3.9 Linux glibc 2.27+ x86-64 Linux glibc 2.28+ x86-64 |
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SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Release files / servalcat-0.4.142-cp39-cp39-macosx_11_0_arm64.whl
| Download URL | servalcat-0.4.142-cp39-cp39-macosx_11_0_arm64.whl |
|---|---|
| Size | 838.4 kB |
| Tags | CPython 3.9 macOS 11.0+ ARM64 |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
Release files / servalcat-0.4.142-cp39-cp39-macosx_10_14_x86_64.whl
| Download URL | servalcat-0.4.142-cp39-cp39-macosx_10_14_x86_64.whl |
|---|---|
| Size | 894.8 kB |
| Tags | CPython 3.9 macOS 10.14+ x86-64 |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.12.9
|
