scipion-em-kiharalab 1.0.1

Scipion plugin in order to use ther kiharalab software

Kihara Lab plugin

This is a Scipion plugin that offers different Kihara Lab tools. These tools will make it possible to carry out different functions for working with electron density maps. The code involving these functionalities can be found at https://github.com/kiharalab.

Therefore, this plugin allows to use programs from the DAQ software suite within the Scipion framework.

Install this plugin

You will need to use Scipion3 to run these protocols.

DAQ, Emap2sec, Emap2sec+, and MainMast are installed automatically by scipion.

Note: Emap2sec+ needs an Nvidia GPU to run.

• Install the stable version

  Through the plugin manager GUI by launching Scipion and following Others >> Plugin Manager

  or

scipion3 installp -p scipion-em-kiharalab

• Developer’s version

  1. Download repository:

  git clone https://github.com/scipion-em/scipion-em-kiharalab.git

  2. Install:

  scipion3 installp -p path_to_scipion-em-kiharalab --devel

Protocols

scipion-em-kiharalab contains the following protocols:

• DAQ model validation: Executes the DAQ software to validate a structure model

• Emap2sec: Identifies protein secondary structures

• segment map: performs the segmentation of maps into different regions by using mainmast software

Packages & enviroments

Packages installed by this plugin can be located in /path/to/scipion/software/em/.

The following packages will be created:

• daq-version

• emap2sec-version

• mainMast-version

Where version is the current version of that specific package.

Also, the following conda enviroments will be created:

• daq-version

• emap2sec-version

• emap2secPlus-version

As of today, Scipion does not automatically uninstall the conda enviroments created in the installation process when uninstalling a plugin, so keep this list in mind if you want to clean up some disk space if you need to uninstall scipion-em-kiharalab.

Changelog

All the recent version changes can be found here.