scipion-em-warp 3.5.0

Plugin to use Warp within the Scipion framework

This plugin provides a wrapper for some of the programs of the Warp software.

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-warp

2. Developer’s version

   • download repository

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

   • install

   scipion installp -p /path/to/scipion-em-warp --devel

Verifying

To check the installation, simply run one of the following Scipion tests:

• scipion3 tests warp.tests.protocols_tomo_tests.TestWarpEstimateCTFTomoReconstruction

• scipion3 tests warp.tests.protocols_tomo_tests.TestDeconvolveTomo

• scipion3 tests warp.tests.test_protocols.TestWarpMotionCorrection

• scipion3 tests warp.tests.test_protocols.TestDeconvolveMics

Protocols

• deconvolve micrographs

• deconvolve tomograms

• deconvolve tilt-series

• tomo reconstruction

• motion correction (for SPA)

• tilt-series motion and ctf estimation (includes ctf estimation and defocus handedness)

References

1. Dimitry Tegunov and Patrick Cramer. Real-time cryo-electron microscopy data preprocessing with Warp. Nature Methods 16(11), 2019, p. 1146-1152.