scipion-em-nysbc 1.0.3

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 at software/em/nysbc3DFSC-2.5, but you can also link an existing installation.

Important: you need to have conda (miniconda3 or anaconda3) pre-installed to use this program.

Configuration variables

CONDA_ACTIVATION_CMD: If undefined, it will rely on conda command being in the PATH (not recommended), which can lead to execution problems mixing scipion python with conda ones. One example of this could can be seen bellow but depending on your conda version and shell you will need something different: CONDA_ACTIVATION_CMD = eval “$(/extra/miniconda3/bin/conda shell.bash hook)”

NYSBC_3DFSC_HOME (default = software/em/nysbc3DFSC-2.5): Path where the 3DFSC is installed.

NYSBC_3DFSC_ACTIVATION_CMD (default = conda activate fsc): Command to activate the 3DFSC environment.

Verifying

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).