{"id":599,"date":"2015-11-24T15:42:26","date_gmt":"2015-11-24T15:42:26","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/icsf\/?page_id=599"},"modified":"2015-11-24T15:43:49","modified_gmt":"2015-11-24T15:43:49","slug":"eman2","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/software\/applications\/eman2\/","title":{"rendered":"eman2"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"http:\/\/blake.bcm.edu\/emanwiki\/EMAN2\">EMAN2<\/a> is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. It performs single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, and also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. EMAN2 is capable of processing very large data sets (>100,000 particle) very efficiently<\/p>\n<p>Note that EMAN2 is the successor to EMAN1 (which is not available on the iCSF).<\/p>\n<p>Version 2.11 of EMAN2 is installed on the iCSF. <\/p>\n<p>MPI support is provided by the <a href=\"http:\/\/ncmi.bcm.edu\/ncmi\/software\/counter_222\/software_121\">PyDusa<\/a> v1.15. This has required a custom build of the CSF OpenMPI 1.6 gcc installation.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>The software is free to use to all iCSF users. However all users make themselves aware of the <a href=\"http:\/\/blake.bcm.tmc.edu\/emanwiki\/EMAN2\/FAQ\/CiteEman2\">citation requirements<\/a> requested by the authors.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the software you must first load <em>one<\/em> of the following modulefiles:<\/p>\n<ul>\n<li>For serial \/ multi-threaded batch jobs and interactive usage:\n<pre>\r\nmodule load apps\/binapps\/eman\/2.11\r\n<\/pre>\n<\/li>\n<li>For small, multi-process jobs\n<pre>\r\nmodule load apps\/binapps\/eman\/2.11-mpi\r\n<\/pre>\n<\/li>\n<\/ul>\n<p>The above modulefiles will automatically load any dependent modulefiles (e.g., mpi).<\/p>\n<h2>Running the application<\/h2>\n<h3>Serial execution<\/h3>\n<p>A number of EMAN2 tools can be run interactively, including <code>e2projectmanager.py<\/code>, <code>e2display.py<\/code> and an interacive python shell <code>e2.py<\/code> (for advanced users). For example,<\/p>\n<pre>\r\ne2projectmanager.py\r\n   #\r\n   # Could also be e2display.py or e2.py for an interactive python shell.\r\n<\/pre>\n<h3>Parallel execution<\/h3>\n<p>It is worth checking with <code>top<\/code> whether anything else is running on the same iCSF node as you before you launch a parallel job. The example below uses 4 cores\/threads<\/p>\n<pre>\r\ne2appname.py --parallel=thread:4 args\r\n    #\r\n    # replace with the required EMAN2 tool (e.g., e2boxer.py)\r\n    # (not all e2 programs support parallel execution)\r\n<\/pre>\n<p>Only single node jobs are possible on iCSF.<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"http:\/\/blake.bcm.tmc.edu\/emanwiki\/EMAN2#Documentation\">EMAN2 Documentation<\/a><\/li>\n<li><a href=\"http:\/\/blake.bcm.tmc.edu\/emanwiki\/EMAN2\/Parallel\">EMAN2 Parallel options<\/a><\/li>\n<li><a href=\"http:\/\/blake.bcm.tmc.edu\/emanwiki\/EMAN2\">EMAN2 website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. It performs single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, and also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. EMAN2 is capable of processing very large data sets (>100,000 particle) very.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/software\/applications\/eman2\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":43,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-599","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/599","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/comments?post=599"}],"version-history":[{"count":2,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/599\/revisions"}],"predecessor-version":[{"id":602,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/599\/revisions\/602"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/43"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/media?parent=599"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}