{"id":3927,"date":"2017-06-16T10:25:47","date_gmt":"2017-06-16T10:25:47","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=3927"},"modified":"2017-06-16T11:43:00","modified_gmt":"2017-06-16T11:43:00","slug":"xcrysden","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/xcrysden\/","title":{"rendered":"XCrySDen"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"http:\/\/www.xcrysden.org\/\">XCrySDen<\/a> (X-Window CRYstalline Structures and DENsities) is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.<\/p>\n<p>Version 1.5.60 is installed on the CSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on accessing this software. It is made available under the GNU GPL v2 license.<\/p>\n<p>The software can be run with the ability to call <a href=\"\/csf-apps\/applications\/crystal\">Crystal<\/a>. To do so, you must be in the <code>crystal<\/code> group on the CSF, which requires that your research group has a Crystal license. See below for more information on running the software with and without Crystal support.<\/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\/gcc\/xcrysden\/1.5.60\r\n<\/pre>\n<p>If you are in the <code>crystal<\/code> unix group and wish to run with Crystal support enabled, you should also load the Crystal modulefile:<\/p>\n<pre>\r\nmodule load apps\/intel-12.0\/crystal\/c09_201_emt64\r\n<\/pre>\n<h3>One-time Setup<\/h3>\n<p>Before running xcrysden for the first time you should copy a config file to your home directory. Please do <em>one<\/em> of the following on the CSF login node:<\/p>\n<ul>\n<li>If NOT using crystal with xcrysden\n<pre>mkdir ~\/.xcrysden\r\ncp $XCRYSDEN_HOME\/custom-definitions ~\/.xcrysden\r\n<\/pre>\n<\/li>\n<li>If using crystal with xcrysden\n<pre>\r\nmkdir ~\/.xcrysden\r\ncp $XCRYSDEN_HOME\/custom-definitions.with-crystal ~\/.xcrysden\/custom-definitions\r\n<\/pre>\n<\/li>\n<\/ul>\n<h2>Running the application<\/h2>\n<p>Ensure you have done the one-time setup above.<\/p>\n<p>Please do not run xcrysden on the login node. Jobs should be run interactively on a compute node using the <code>qrsh<\/code> command. You must have logged in to the CSF with <em>X11 forwarding<\/em> enabled. Please see the <a href=\"\/csf2\/getting-started-on-the-csf\/using-an-app-with-a-gui-x11-and-qrsh\/\">interactive guide<\/a> for more details.<\/p>\n<h3>Interactive usage<\/h3>\n<p>Start an interactive session from the login node:<\/p>\n<pre>\r\nqrsh -l inter -l short\r\n<\/pre>\n<p>Wait until you are logged in to a backend compute node, then:<\/p>\n<pre>\r\nmodule load apps\/gcc\/xcrysden\/1.5.60\r\n\r\n# Optional if using crystal\r\nmodule load apps\/intel-12.0\/crystal\/c09_201_emt64\r\n\r\n# Start xcrysden\r\nxcrysden\r\n<\/pre>\n<h3>X11 Errors<\/h3>\n<p>If you receive errors about X11, for example:<\/p>\n<pre>\r\nX Error of failed request: BadValue\r\n<\/pre>\n<p>then please try setting the following environment variable just <em>before<\/em> running <code>xcrysden<\/code>:<\/p>\n<pre>\r\nexport LIBGL_ALWAYS_INDIRECT=1\r\n<\/pre>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"http:\/\/www.xcrysden.org\/\">xcrysden website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview XCrySDen (X-Window CRYstalline Structures and DENsities) is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. Version 1.5.60 is installed on the CSF. Restrictions on use There are no restrictions on accessing this software. It is made available under the GNU GPL v2 license. The software can be run with the ability to call Crystal. To do.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/xcrysden\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-3927","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/3927","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=3927"}],"version-history":[{"count":6,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/3927\/revisions"}],"predecessor-version":[{"id":3936,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/3927\/revisions\/3936"}],"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=3927"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}