This plugin provides a wrapper for Gctf program.
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:
Stable version
scipion installp -p scipion-em-gctf
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 inscipion.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 fromGctf_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
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.
- ctf estimation
- ctf refinement
- tilt-series gctf
- Zhang K. (2016). Gctf: Real-time CTF determination and correction. JSB, 193: 1-12.