{"id":2958,"date":"2019-04-02T11:51:19","date_gmt":"2019-04-02T10:51:19","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=2958"},"modified":"2025-09-26T14:52:54","modified_gmt":"2025-09-26T13:52:54","slug":"pymol","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/pymol\/","title":{"rendered":"Pymol"},"content":{"rendered":"<div class=\"warning\">This package does not work on CSF3. This page has been left intact in case it is helpful to previous researchers\/students. We do not have a license.<\/div>\n<h2>Overview<\/h2>\n<p>A molecular visualisation tool.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>Previously we had an educational-use-only version installed for usage in accordance with the <a href=\"http:\/\/www.pymol.org\/educational\">policy on the software vendor website<\/a>. Usage of this software was restricted to one research group. However this version <strong>no longer works<\/strong> on the CSF.<\/p>\n<p>Hence we have compiled the open-source version of PyMOL. This doesn&#8217;t have all of the features of the commerical\/educational release but can be used by any CSF user.<\/p>\n<p>Version 2.3.0 (open-source) is installed on CSF3.<\/p>\n<h2>Set up procedure<\/h2>\n<p>You will need to connect to CSF3 using <code>ssh -X<\/code> to have the display exported to your local machine. <\/p>\n<p>You should then load the pymol module:<\/p>\n<pre>module load apps\/gcc\/pymol\/2.3.0<\/pre>\n<h2>Running the application<\/h2>\n<p>The software is launched using the command <code>pymol<\/code>. It can be run interactively (via its GUI) or in batch via the usual job-script method. Examples are given below. To see what command-line flags are available, run the following command on the login node after loading the modulefile:<\/p>\n<pre>\r\npymol --help\r\n<\/pre>\n<p>Normal use of pymol should <strong>not<\/strong> use the login node &#8211; it must be run on a compute node.<\/p>\n<h3>Interactive Usage<\/h3>\n<p>If you need to run the software interactively you must do so via a compute node using <a href=\"\/csf3\/batch\/qrsh\">qrsh<\/a> e.g:<\/p>\n<pre>\r\nqrsh -l short -V -cwd pymol\r\n<\/pre>\n<p>Alternatively, log in to the compute node first and then setup and run pymol<\/p>\n<pre>\r\nqrsh -l short\r\n #\r\n # Wait until you have been logged in to t a compute node, then:\r\nmodule load apps\/gcc\/pymol\/2.3.0\r\npymol\r\n<\/pre>\n<h3>Batch Usage<\/h2>\n<p>To run pymol in a batch job, without the GUI, create a jobscript similar to the following:<\/p>\n<pre>\r\n#!\/bin\/bash --login\r\n#$ -cwd\r\n#$ -pe smp.pe 8        # Optional line (e.g., use 8 cores). Delete line for a serial job.\r\nmodule load apps\/gcc\/pymol\/2.3.0\r\n\r\npymol -c -d \"set max_threads, $NSLOTS\" -r myscript.py\r\n                               #\r\n                               # This will tell pymol to use the number of cores\r\n                               # specified above (or 1 for a serial job)\r\n<\/pre>\n<p>Submit you job to the batch system using<\/p>\n<pre>\r\nqsub <em>myjobscript<\/em>\r\n<\/pre>\n<p>where <code><em>myjobscript<\/em><\/code> is the name of your jobscript file.<\/p>\n<h2>Further info<\/h2>\n<p>The <a href=\"http:\/\/www.pymol.org\/support\">pymol website<\/a> has a variety of resources available including <a href=\"http:\/\/www.pymolwiki.org\/index.php\/Main_Page\">a user maintained wiki.<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>This package does not work on CSF3. This page has been left intact in case it is helpful to previous researchers\/students. We do not have a license. Overview A molecular visualisation tool. Restrictions on use Previously we had an educational-use-only version installed for usage in accordance with the policy on the software vendor website. Usage of this software was restricted to one research group. However this version no longer works on the CSF. Hence we.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/pymol\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":6,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-2958","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2958","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=2958"}],"version-history":[{"count":3,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2958\/revisions"}],"predecessor-version":[{"id":11031,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2958\/revisions\/11031"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=2958"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}