scipion-em-gctf 3.2

Plugin to use Gctf program within the Scipion framework

This plugin provides a wrapper for Gctf program.

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-gctf

2. Developer’s version

   • download repository

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

   • install

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

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 below but depending on your conda version and shell you will need something different: CONDA_ACTIVATION_CMD = eval “$(/extra/miniconda3/bin/conda shell.bash hook)”

GCTF_ENV_ACTIVATION (default = conda activate gctf): Command to activate the Gctf environment. It will have cudatoolkit=10.1 installed.

GCTF_HOME (default = software/em/gctf-1.18): Path to Gctf installation folder.

GCTF_BIN (default = Gctf_v1.18_sm30-75_cu10.1): Binary to use.

Verifying

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

scipion test gctf.tests.test_protocols_gctf.TestGctf
scipion tests gctf.tests.test_protocols_gctf_ts.TestGctfTs

Supported versions

1.18

Protocols

• ctf estimation

• tilt-series gctf

References

1. Zhang K. (2016). Gctf: Real-time CTF determination and correction. JSB, 193: 1-12.