This plugin provide wrappers around Gctf program.
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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-gctfDeveloper’s version
download repository
git clone https://github.com/scipion-em/scipion-em-gctf.gitinstall
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.TestGctfSupported 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
References
Zhang K. (2016). Gctf: Real-time CTF determination and correction. JSB, 193: 1-12.
2 maintainers
Release files for scipion-em-gctf 3.0.11
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| scipion-em-gctf-3.0.11.tar.gz | 39.2 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scipion_em_gctf-3.0.11-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 87.5 kB
Release files / scipion-em-gctf-3.0.11.tar.gz
| Download URL | scipion-em-gctf-3.0.11.tar.gz |
|---|---|
| Size | 39.2 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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twine/3.2.0 pkginfo/1.6.1 requests/2.23.0 setuptools/49.2.1 requests-toolbelt/0.9.1 tqdm/4.51.0 CPython/3.9.0
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Release files / scipion_em_gctf-3.0.11-py3-none-any.whl
| Download URL | scipion_em_gctf-3.0.11-py3-none-any.whl |
|---|---|
| Size | 48.3 kB |
| Tags | Python 3 |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.2.0 pkginfo/1.6.1 requests/2.23.0 setuptools/49.2.1 requests-toolbelt/0.9.1 tqdm/4.51.0 CPython/3.9.0
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