{ "info": { "author": "Grigory Sharov", "author_email": "sharov.grigory@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", "Programming Language :: Python :: 2.7" ], "description": "============\nEMAN2 plugin\n============\n\nThis plugin provide wrappers around several programs of `EMAN2 `_ software suite.\n\n.. figure:: http://scipion-test.cnb.csic.es:9980/badges/eman2_devel.svg\n :align: left\n :alt: build status\n\nInstallation\n------------\n\nYou will need to use `2.0 `_ version of Scipion to be able to run these protocols. To install the plugin, you have two options:\n\na) Stable version\n\n.. code-block::\n\n scipion installp -p scipion-em-eman2\n\nb) Developer's version\n\n * download repository\n\n .. code-block::\n\n git clone https://github.com/scipion-em/scipion-em-eman2.git\n\n * install\n\n .. code-block::\n\n scipion installp -p path_to_scipion-em-eman2 --devel\n\nEMAN2 binaries will be installed automatically with the plugin, but you can also link an existing installation.\n\n * Default installation path assumed is ``software/em/eman-2.3``, if you want to change it, set *EMAN2_HOME* in ``scipion.conf`` file pointing to the folder where the EMAN2 is installed.\n\n **IMPORTANT: From plugin version 1.0.5 EMAN2DIR was renamed to EMAN2_HOME. Please update your scipion.conf file!**\n\n * If you need to pass special options to mpirun (like a hostfile), you can use the *EMANMPIOPTS* shell variable, but most users should not need this. A typical usage would be ``export EMANMPIOPTS=\"-hostfile myhosts.txt\"``. You should only do this if necessary, though (note that then when supplying the parameter **--parallel=mpi:n:scratch_directory**, 'n' is no longer the number of cpus to use, but rather the number of nodes listed in myhosts.txt).\n * The default scratch directory is assumed */tmp/*. You can change it by setting *EMAN2SCRATCHDIR* in your shell environment.\n\nTo check the installation, simply run one of the following Scipion tests:\n\n.. code-block::\n\n scipion test eman2.tests.test_protocols_eman.TestEmanTiltValidate\n scipion test eman2.tests.test_protocols_eman.TestEmanRefineEasy\n scipion test eman2.tests.test_protocols_eman.TestEmanRefine2DBispec\n scipion test eman2.tests.test_protocols_eman.TestEmanRefine2D\n scipion test eman2.tests.test_protocols_eman.TestEmanReconstruct\n scipion test eman2.tests.test_protocols_eman.TestEmanInitialModelMda\n scipion test eman2.tests.test_protocols_eman.TestEmanInitialModelGroel\n scipion test eman2.tests.test_protocols_eman.TestEmanInitialModelSGD\n scipion test eman2.tests.test_protocols_eman.TestEmanCtfAuto\n scipion test eman2.tests.test_protocols_eman.TestEmanAutopick\n\nA complete list of tests can also be seen by executing ``scipion test --show --grep eman``\n\nSupported versions\n------------------\n\n2.21, 2.3\n\nIn 2018 the plugin was updated to support the latest (at that moment) EMAN2: 2.21. This required a lot of code refactoring and the support of old EMAN2 version 2.11 had to be discontinued. Several new protocols were added: 2D refinements, tilt validation, ctf-auto and new e2boxer. The full changelog since Scipion-1.x is available `here `_.\n\nProtocols\n---------\n\n* `boxer (old and new interactive e2boxer.py) `_\n* boxer auto (fully automated new boxer in >=2.21)\n* ctf auto\n* `initial model `_\n* initial model SGD\n* reconstruct\n* refine 2d\n* refine 2d bispec\n* refine easy\n* `sparx picker `_\n* tilt validate\n\nReferences\n----------\n\n1. \\G. Tang, L. Peng, P.R. Baldwin, D.S. Mann, W. Jiang, I. Rees & S.J. Ludtke. (2007) EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol. 157, 38-46. 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