scipion-em-cistem 3.9.1

Plugin to use cisTEM programs within the Scipion framework

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:

1. Stable version

scipion installp -p scipion-em-cistem

2. Developer’s version

   • download repository

   git clone -b devel https://github.com/scipion-em/scipion-em-cistem.git

   • install

   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

1. 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

2. Timothy Grant and Alexis Rohou and Nikolaus Grigorieff. (2018) cisTEM, user-friendly software for single-particle image processing. eLife 7:e35383.