===========
Gctf plugin
===========
This plugin provides a wrapper for `Gctf <https://www2.mrc-lmb.cam.ac.uk/research/locally-developed-software/zhang-software/>`_ program.
.. image:: https://img.shields.io/pypi/v/scipion-em-gctf.svg
:target: https://pypi.python.org/pypi/scipion-em-gctf
:alt: PyPI release
.. image:: https://img.shields.io/pypi/l/scipion-em-gctf.svg
:target: https://pypi.python.org/pypi/scipion-em-gctf
:alt: License
.. image:: https://img.shields.io/pypi/pyversions/scipion-em-gctf.svg
:target: https://pypi.python.org/pypi/scipion-em-gctf
:alt: Supported Python versions
.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-gctf?server=https%3A%2F%2Fsonarcloud.io
:target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-gctf
:alt: SonarCloud quality gate
.. image:: https://img.shields.io/pypi/dm/scipion-em-gctf
:target: https://pypi.python.org/pypi/scipion-em-gctf
:alt: Downloads
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:
a) Stable version
.. code-block::
scipion installp -p scipion-em-gctf
b) Developer's version
* download repository
.. code-block::
git clone -b devel https://github.com/scipion-em/scipion-em-gctf.git
* install
.. code-block::
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:
.. code-block::
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.
Raw data
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