scipion-em-locscale 3.0.5

Plugin to use Locscale program within the Scipion framework

This plugin provides a wrapper around LocScale program for local sharpening of cryo-EM density maps.

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-locscale

2. Developer’s version

   • download repository

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

   • install

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

LocScale sources will be downloaded automatically with the plugin, but you can also link an existing installation. Default installation path assumed is software/em/locscale-0.1, if you want to change it, set LOCSCALE_HOME in scipion.conf file to the folder where the LocScale is installed. LocScale uses EMAN2 libraries, so you need to provide existing EMAN2 installation path by setting EMAN2_HOME variable (default eman-2.99) in the config file.

Note: mpi4py will be installed in the Eman’s python

Note2: File locscale-0.1/source/locscale_mpi.py has been patched (see locscale_mpi.py.patch) to be able to work with new versions of EMAN

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

scipion test locscale.tests.test_protocol_locscale.TestProtLocscale

A complete list of tests can also be seen by executing scipion test --show --grep locscale

Supported versions

0.1

Protocols

• local sharpening

References

1. Jakobi A. et al., eLife, 2017