{"id":690,"date":"2019-01-02T19:44:52","date_gmt":"2019-01-02T19:44:52","guid":{"rendered":"http:\/\/www.clowersresearch.com\/main\/?p=690"},"modified":"2019-01-02T20:09:05","modified_gmt":"2019-01-02T20:09:05","slug":"conformational-searching-using-python","status":"publish","type":"post","link":"http:\/\/www.clowersresearch.com\/main\/conformational-searching-using-python\/","title":{"rendered":"Conformational Searching using Python"},"content":{"rendered":"\n<p>This is the first of a series examining the use of python to generate candidate structures of molecules. These conformations may serve a variety of functions, though our particular purpose is to identify candidates for additional optimization and ultimate use in ion mobility modeling experiments. After considering a range of tools (e.g. Avogadro or ChemDraw), it was apparent that a more automated, open-source work-flow was needed. In full disclosure, there are surely other mechanisms to make this happen but the following<a href=\"https:\/\/jupyter.org\/\"> jupyter <\/a>notebook is a reasonable approach. Visualization of the conformers can be accomplished using <a href=\"https:\/\/pymol.org\/2\/\">pymol<\/a> if you that module is installed and a server instance running in the background (i.e. pymol -R).<\/p>\n<p>\n<script src=\"https:\/\/gist.github.com\/bhclowers\/8b263305368825549cb0f4dbd099bae7.js\"><\/script><\/p>\n","protected":false},"excerpt":{"rendered":"<p>This is the first of a series examining the use of python to generate candidate structures of molecules. These conformations may serve a variety of functions, though our particular purpose is to identify candidates for additional optimization and ultimate use in ion mobility modeling experiments. After considering a range of tools (e.g. Avogadro or ChemDraw), [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":705,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"spay_email":""},"categories":[6,11],"tags":[4,25],"jetpack_featured_media_url":"http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/txas.png","_links":{"self":[{"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/posts\/690"}],"collection":[{"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/comments?post=690"}],"version-history":[{"count":10,"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/posts\/690\/revisions"}],"predecessor-version":[{"id":700,"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/posts\/690\/revisions\/700"}],"wp:featuredmedia":[{"embeddable":true,"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/media\/705"}],"wp:attachment":[{"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/media?parent=690"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/categories?post=690"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/tags?post=690"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}