{"id":437,"date":"2016-09-30T14:38:37","date_gmt":"2016-09-30T21:38:37","guid":{"rendered":"https:\/\/bionmr.mbi.ucla.edu\/?page_id=437"},"modified":"2016-10-06T16:25:28","modified_gmt":"2016-10-06T23:25:28","slug":"processing-with-hmsisttopspin-3","status":"publish","type":"page","link":"https:\/\/bionmr.mbi.ucla.edu\/?page_id=437","title":{"rendered":"Processing with hmsIST\/TopSpin 3"},"content":{"rendered":"<p>NUS data can be processed using hmsIST\u00a0<em>inside TopSpin3<\/em>, but only if the data was acquired in TopSpin3.<\/p>\n<p>For 2D data, run the AU program <span style=\"color: #800000;\">xfb_hmsIST<\/span>. For 3D data, run the AU program <span style=\"color: #800000;\">xf3d_hmsIST<\/span>.<\/p>\n<p>It will ask you a few simple questions:<\/p>\n<ul>\n<li>Perform f2 and f1 transform after reconstruction: \u00a0 y<\/li>\n<li>Perform abs after f3 transform: \u00a0 y<\/li>\n<li>Enter chemical shift of water in ppm: \u00a0 4.7 \u00a0 \u00a0(or whatever it is)<\/li>\n<li>Enter distance from water in ppm: \u00a0 default is 0.1 \u00a0&#8211; this is the region around water that you DON&#8217;T want it to try to baseline correct. (I usually set it to 0.3)<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><strong>If the data acquisition halted early<\/strong> (before finishing) &#8211; and if the NUS schedule was random:<\/p>\n<p>You can still process with <span style=\"color: #800000;\">xfb_hmsIST<\/span> or <span style=\"color: #800000;\">xf3d_hmsIST<\/span>.<\/p>\n<p>For example: an hncacb with TD: \u00a0 F3:2048 \u00a0 F2:80 \u00a0 F1:200, \u00a0 NusAMOUNT = 25% (<span style=\"color: #800000;\">NusPOINTS = 1000<\/span>).<\/p>\n<p>Say this experiment got stopped after only <span style=\"color: #800000;\">340 NusPOINTS<\/span> were collected. To process this, edit the nuslist. This file has the sampling schedule, and will have 1000 lines in it. Truncate this file so that it only has <span style=\"color: #800000;\">340 lines<\/span>. Also, in eda, set NusAMOUNT\/NusPOINTS such that <span style=\"color: #800000;\">NusPOINTS = 340<\/span>. Then you can process it normally using xf3d_hmsIST.<\/p>\n<p>&nbsp;<\/p>\n<p><a href=\"https:\/\/bionmr.mbi.ucla.edu\/?page_id=408\">back to Non-Uniform Sampling Experiments<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>NUS data can be processed using hmsIST\u00a0inside TopSpin3, but only if the data was acquired in TopSpin3. For 2D data, run the AU program xfb_hmsIST. For 3D data, run the AU program xf3d_hmsIST. It will ask you a few simple questions: Perform f2 and f1 transform after reconstruction: \u00a0 y Perform abs after f3 transform: [&hellip;]<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-437","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/bionmr.mbi.ucla.edu\/index.php?rest_route=\/wp\/v2\/pages\/437","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/bionmr.mbi.ucla.edu\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/bionmr.mbi.ucla.edu\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/bionmr.mbi.ucla.edu\/index.php?rest_route=\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/bionmr.mbi.ucla.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=437"}],"version-history":[{"count":4,"href":"https:\/\/bionmr.mbi.ucla.edu\/index.php?rest_route=\/wp\/v2\/pages\/437\/revisions"}],"predecessor-version":[{"id":465,"href":"https:\/\/bionmr.mbi.ucla.edu\/index.php?rest_route=\/wp\/v2\/pages\/437\/revisions\/465"}],"wp:attachment":[{"href":"https:\/\/bionmr.mbi.ucla.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=437"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}