scipion-em-nysbc 1.0.2b0

Plugin to use NYSBC programs within the Scipion framework

This plugin provide a wrapper around 3DFSC program developed at Salk Institute and NYSBC.

Installation

You will need to use 2.0 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-nysbc

2. Developer’s version

   • download repository

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

   • install

   scipion installp -p path_to_scipion-em-nysbc --devel

3DFSC binaries will be installed automatically with the plugin, but you can also link an existing installation. Important: you need to have conda (miniconda3 or anaconda3) pre-installed to use this program. Default installation path assumed is software/em/nysbc3DFSC-2.5, if you want to change it, set NYSBC_3DFSC_HOME in scipion.conf file to the folder where the 3DFSC is installed.

To check the installation, simply run the following Scipion test: scipion test nysbc.tests.test_protocols_nysbc.TestNysbc3DFSC

Supported versions

2.5, 3.0

Protocols

• 3d fsc

References

1. Yong Zi Tan, Philip R Baldwin, Joseph H Davis, James R Williamson, Clinton S Potter, Bridget Carragher & Dmitry Lyumkis. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nature Methods volume 14, pages 793–796 (2017).