This plugin provides wrappers for several programs of cisTEM software suite.
Installation
You will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:
Stable version
scipion installp -p scipion-em-cistemDeveloper’s version
download repository
git clone -b devel https://github.com/scipion-em/scipion-em-cistem.gitinstall
scipion installp -p /path/to/scipion-em-cistem --devel
Important: Starting from plugin v3.9, the config variables have been renamed. See: scipion3 config -p cistem
cisTEM binaries will be installed automatically with the plugin, but you can also link an existing installation.
Default installation path assumed is software/em/cistem-1.0.0-beta, if you want to change it, set CISTEM_HOME in scipion.conf file pointing to the folder where the cisTEM is installed.
It’s possible to use CTFFIND installed separately from cisTEM by defining CTFFIND_HOME variable in scipion.conf. Setting this value will have the priority over Ctffind inside cisTEM.
A complete list of tests can be seen by executing scipion test --show --grep cistem
Supported versions
1.0.0-beta (cistem)
4.1.13, 4.1.14 (ctffind4)
5.0 (ctffind5)
Licenses
cistem binaries are distributed under The Janelia Research Campus Software License 1.2 license
ctffind4 binaries are distributed under The Janelia Research Campus Software License 1.1 license
ctffind5 binaries are distributed under The Janelia Research Campus Software License 1.2 license
Protocols
ctffind
import tomo CTFs
tilt-series ctffind
unblur
find particles
classify 2D
References
Johannes Elferich, Lingli Kong, Ximena Zottig, Nikolaus Grigorieff. (2024) CTFFIND5 provides improved insight into quality, tilt and thickness of TEM samples. bioRxiv 2024.02.26.582023; doi: https://doi.org/10.1101/2024.02.26.582023
Timothy Grant and Alexis Rohou and Nikolaus Grigorieff. (2018) cisTEM, user-friendly software for single-particle image processing. eLife 7:e35383.
1 maintainer
Metadata
1 maintainer
Release files for scipion-em-cistem 3.9.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| scipion-em-cistem-3.9.1.tar.gz | 160.3 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scipion_em_cistem-3.9.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 333.9 kB
Release files / scipion-em-cistem-3.9.1.tar.gz
| Download URL | scipion-em-cistem-3.9.1.tar.gz |
|---|---|
| Size | 160.3 kB |
| Tags | Source |
|
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/5.0.0 CPython/3.8.18
|
Release files / scipion_em_cistem-3.9.1-py3-none-any.whl
| Download URL | scipion_em_cistem-3.9.1-py3-none-any.whl |
|---|---|
| Size | 173.6 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.0.0 CPython/3.8.18
|
