{"id":3057,"date":"2016-06-02T13:32:29","date_gmt":"2016-06-02T13:32:29","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=3057"},"modified":"2016-06-02T13:34:14","modified_gmt":"2016-06-02T13:34:14","slug":"pycoco","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/pycoco\/","title":{"rendered":"PyCoCo"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/bitbucket.org\/extasy-project\/coco\">PyCoCo<\/a> (&#8220;Complementary Coordinates&#8221;) is a method for testing and potentially enriching the variety of conformations within an ensemble of molecular structures.<\/p>\n<p>Version 0.3.0 is installed on the CSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on accessing this software on the CSF. Please reference the following if using PyCoCo in your work:<\/p>\n<p><a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/prot.22235\/abstract\">Laughton C.A., Orozco M. and Vranken W., COCO: A simple tool to enrich the representation of conformational variability in NMR structures, PROTEINS, 75, 206-216 (2009)<\/a><\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the software you must first load the modulefile:<\/p>\n<pre>\r\nmodule load apps\/binapps\/extasy_coco\/0.3.0\r\n<\/pre>\n<p>This will automatically load the Anaconda Python (v2.3.0) modulefile which provides python 2.7.10.<\/p>\n<h2>Running the application<\/h2>\n<p>Please do not run pyCoCo on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n\r\n## This is a serial jobscript (1 core) so turn off MPI parallelism with --nompi\r\npyCoCo --nompi -i <em>INPUT<\/em> -t <em>TOPOLOGY<\/em> -o <em>OUTPUT<\/em>\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h3>Parallel batch job submission<\/h3>\n<p>Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n#$ -pe smp.pe 4     # Single-node multi-core jobs (number of cores can be 2-24)\r\n\r\n## $NSLOTS is automatically set to the number of cores given above\r\nmpirun -n $NSLOTS pyCoCo -i <em>INPUT<\/em> -t <em>TOPOLOGY<\/em> -o <em>OUTPUT<\/em>\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"https:\/\/bitbucket.org\/extasy-project\/coco\">PyCoCo website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview PyCoCo (&#8220;Complementary Coordinates&#8221;) is a method for testing and potentially enriching the variety of conformations within an ensemble of molecular structures. Version 0.3.0 is installed on the CSF. Restrictions on use There are no restrictions on accessing this software on the CSF. Please reference the following if using PyCoCo in your work: Laughton C.A., Orozco M. and Vranken W., COCO: A simple tool to enrich the representation of conformational variability in NMR structures, PROTEINS,.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/pycoco\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-3057","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/3057","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=3057"}],"version-history":[{"count":3,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/3057\/revisions"}],"predecessor-version":[{"id":3061,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/3057\/revisions\/3061"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=3057"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}