scipion-em-gapstop 3.0.0

Plugin to use gapstop within the Scipion framework

This plugin provides a wrapper around the program GAPSTOP_TM (GPU-Accelerated Python STOPgap for Template Matching) to use it within Scipion framework. The library cryoCAT is also integrated as part of the plugin.

Installation

You will need to use 3.0 version of Scipion to run these protocols. To install the plugin, you have two options:

1. Stable version:

scipion3 installp -p scipion-em-gapstop

2. Developer’s version

   • download the repository from github:

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

   • install:

   scipion3 installp -p /path/to/scipion-em-gapstop --devel

To check the installation, simply run the following Scipion test for the plugin:

scipion3 tests gapstop.tests.tests_gapstop.Testgapstop

To check the installation, simply run one of the tests. A complete list of tests can be displayed by executing

scipion3 tests --grep gapstop --show

Protocols

• Template matching : Generate score and angular maps from the introduced tomograms from which the coordinates can be extracted with the protocol ‘Extract coordinates’.

• Extract coordinates : Extracts coordinates from score maps produced by template matching with GAPSTOP(TM).

Latest plugin versions

If you want to check the latest version and release history go to CHANGES

References

1. Cruz-León, S., Majtner, T., Hoffmann, P.C. et al. Nat Commun 15, 3992 (2024).