scipion-em-gctf

Plugin to use Gctf program within the Scipion framework

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Project description

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:

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 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

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

Project details

These details have not been verified by PyPI

Project links

GitHub Statistics

View statistics for this project via Libraries.io, or by using our public dataset on Google BigQuery

Release history Release notifications | RSS feed

This version

3.1.3

Nov 19, 2023

3.1.2

Dec 27, 2022

3.1.1

Aug 7, 2022

3.1

Jul 22, 2022

3.0.16

Jul 16, 2022

3.0.15

Apr 19, 2022

3.0.14

Apr 4, 2022

3.0.13

Nov 13, 2021

3.0.12

Jan 21, 2021

3.0.11

Oct 31, 2020

3.0.10

Sep 21, 2020

3.0.9

Jun 5, 2020

1.0.9

May 31, 2020

1.0.8

Apr 16, 2020

1.0.7

Aug 2, 2019

1.0.6

Apr 8, 2019

1.0.4

Mar 1, 2019

1.0.3

Feb 10, 2019

1.0.2

Oct 21, 2018

1.0.1

Oct 14, 2018

1.0.0

Oct 13, 2018

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Source Distribution

scipion-em-gctf-3.1.3.tar.gz (40.7 kB view hashes)

Uploaded Nov 19, 2023 Source

Built Distribution

scipion_em_gctf-3.1.3-py3-none-any.whl (50.9 kB view hashes)

Uploaded Nov 19, 2023 Python 3

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