scipion-em/scipion-em-gctf

Plugin to use Gctf program within the Scipion framework

Gctf plugin

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
   

• Gctf binaries will be installed automatically with the plugin, but you can also link an existing installation. Default installation path assumed is software/em/gctf-1.18, if you want to change it, set GCTF_HOME in scipion.conf file to the folder where the Gctf is installed. Depending on your CUDA version and GPU card compute capability you might want to change the default binary from Gctf_v1.18_sm30-75_cu10.1 to a different one by explicitly setting GCTF variable.
• If you need to use CUDA different from the one used during Scipion installation (defined by CUDA_LIB), you can add GCTF_CUDA_LIB variable to the config file. Various binaries can be downloaded from the official Gctf website.

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

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

Supported versions

1.06 and 1.18.

1.18 is a special version designed for VPP data, it does not support local/movie CTF refinement or validation options.

Protocols

• ctf estimation
• ctf refinement
• tilt-series gctf

References

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