Plugin to use Locscale program within the Scipion framework
Project description
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:
Stable version
scipion installp -p scipion-em-locscale
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
Jakobi A. et al., eLife, 2017
Project details
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