Skip to content
Plugin to use Localrec programs within the Scipion framework
Branch: master
Clone or download
Latest commit 9d77e49 May 23, 2019
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
localrec Added plugin configuration file for protocols tree Jan 8, 2019
.gitignore updating .gitignore Nov 21, 2018
CHANGES.txt Add pip module files Aug 27, 2018
LICENCE Add pip module files Aug 27, 2018
MANIFEST.in Include protocol.conf to create the source distribution Mar 1, 2019
README.rst Update README.rst May 23, 2019
setup.py * Modify the README file Apr 1, 2019

README.rst

Localrec scipion plugin

Electron cryomicroscopy can yield near-atomic resolution structures of highly ordered macromolecular complexes. Often however some subunits bind in a flexible manner, have different symmetry from the rest of the complex, or are present in sub-stoichiometric amounts, limiting the attainable resolution. Here we implement a general method for the localized three-dimensional reconstruction of such subunits. (see http://www.opic.ox.ac.uk/wiki/index.php/Localized_reconstruction for details)

This sub-package contains data and protocol classes to use Localrec within the Scipion framework

Install this plugin

You will need to use 2.0.0 version of Scipion to run these protocols. To install the plugin, you have two options:

  • Stable version
scipion installp -p scipion-em-localrec

OR

  • through the plugin manager GUI by launching Scipion and following Configuration >> Plugins
  • Developer's version
  1. Download repository:
git clone https://github.com/scipion-em/scipion-em-localrec.git
  1. Install:
scipion installp -p path_to_scipion-em-localrec --devel
  • Tests
  1. scipion test localrec.tests.test_protocol_localized_reconstruction

Protocols

  • localized subparticles: Calculate the orientations of the subunits of interest and their positions in the original particle images.
  • filter_subunits: Filter the subunits (sub-particles) based on spatial distance, angular distance, etc.
  • localized extraction: Extract computed sub-particles from a SetOfParticles.

Buildbot status

Status devel version:

Status production version:

You can’t perform that action at this time.