Scipion plugin for EMAN2 Tomography
This plugin provide wrappers around several programs of EMAN2 tomography software suite.
Installation
The plugin can be installed in user (stable) or developer (latest, may be unstable) mode:
1. User (stable) version::
scipion3 installp -p scipion-em-emantomo2. Developer (latest, may be unstable) version::
Clone the source code repository:
git clone https://github.com/scipion-em/scipion-em-emantomo.gitMove to devel branch:
git checkout develInstall:
scipion3 installp -p local/path/to/scipion-em-emantomo --develProtocols
The integrated protocols are:
Tilt series alignment and tomograms reconstruction.
CTF estimation.
Tomogram clipping.
Subtomograms manual picking.
Template matching picking.
Average subtomograms.
Subtomograms extraction from the tomograms.
Subtomograms extraction from the tilt series.
Initial model.
New initial model (from particles extracted from the tilt series).
Subtomograms refinement.
New subtomograms refinement (from particles extracted from the tilt series).
New multi-reference classification of subtomograms (from particles extracted from the tilt series).
Tests
The installation can be checked out running some tests. To list all of them, execute:
scipion3 tests --grep emantomoTo run all of them, execute:
scipion3 tests --grep emantomo --runTo run a specific test, for example, the tests to check the protocol for averaging subtomograms (the following command can be copied from the test list displayed when listing the tests, as explained above):
scipion3 tests emantomo.tests.test_protocols_sta_classic_workflow.TestEmanTomoAverageSubtomogramsStaClassicTutorial
The workflow test generates a emantomo workflow that offers an overview of how to use emantomo.
scipion3 tests emantomo.tests.test_protocols_sta_classic_workflowReferences
Single particle tomography in EMAN2. Jesús G. Galaz-Montoya et al., Journal of Structural Biology, 2015.
High resolution single particle refinement in EMAN2.1. James M. Bell et al., Methods, 2016.
Contact information
If you experiment any problem, please contact us here: scipion-users@lists.sourceforge.net or open an issue.
We’ll be pleased to help.
Scipion Team
1 maintainer
Metadata
1 maintainer
Release files for scipion-em-emantomo 3.4.3
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_emantomo-3.4.3.tar.gz | 147.3 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scipion_em_emantomo-3.4.3-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 336.0 kB
Release files / scipion_em_emantomo-3.4.3.tar.gz
| Download URL | scipion_em_emantomo-3.4.3.tar.gz |
|---|---|
| Size | 147.3 kB |
| Tags | Source |
|
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Release files / scipion_em_emantomo-3.4.3-py3-none-any.whl
| Download URL | scipion_em_emantomo-3.4.3-py3-none-any.whl |
|---|---|
| Size | 188.6 kB |
| Tags | Python 3 |
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SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
twine/6.1.0 CPython/3.8.18
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