{"id":98,"date":"2020-04-28T10:55:24","date_gmt":"2020-04-28T10:55:24","guid":{"rendered":"http:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/getting-data-from-resource-name\/"},"modified":"2020-10-23T12:04:41","modified_gmt":"2020-10-23T12:04:41","slug":"volume-pre-processing","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/volume-pre-processing\/","title":{"rendered":"Volume pre-processing"},"content":{"rendered":"\n<p>When preparing to match two volumes from different sources, there are a number of&nbsp;pre-processing&nbsp;steps that help the comparison:<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Bandpass&nbsp;filtering<\/h3>\n\n\n\n<p>The resolution range of the higher resolution volume will typically be restricted to that of the lower resolution volume, since the higher resolution information cannot be matched.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Background peak<\/h3>\n\n\n\n<p>The distribution of density values in the map typically has a peak representing the large number of voxels having a background value. The map values are all shifted by a constant amount so that this peak appears at zero.<\/p>\n\n\n\n<div class=\"wp-block-image\"><figure class=\"aligncenter size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"689\" height=\"420\" src=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-content\/uploads\/sites\/154\/2020\/10\/fig5.png\" alt=\"\" class=\"wp-image-184\" srcset=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-content\/uploads\/sites\/154\/2020\/10\/fig5.png 689w, https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-content\/uploads\/sites\/154\/2020\/10\/fig5-300x183.png 300w\" sizes=\"auto, (max-width: 689px) 100vw, 689px\" \/><figcaption><strong>Figure 5<\/strong>\u00a0Distribution of map values, illustrating the background peak at zero. Plots are copied from the Advanced Validation pages of the corresponding EMDB entries.<\/figcaption><\/figure><\/div>\n\n\n\n<h3 class=\"wp-block-heading\">Contour level<\/h3>\n\n\n\n<p>The map contains a continuous range of values at its grid positions. While high values are expected to represent the macromolecule and low values the surrounding solvent, there is no explicit division between the two. When interpreting a map, software will often set a contour level that represents the boundary between molecule and solvent, but this choice is somewhat subjective. Typically, it is chosen so that the enclosed volume corresponds to the known molecular weight at a typical molecular density.<\/p>\n\n\n\n<div class=\"wp-block-image\"><figure class=\"aligncenter size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"687\" height=\"515\" src=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-content\/uploads\/sites\/154\/2020\/10\/fig6.png\" alt=\"\" class=\"wp-image-186\" srcset=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-content\/uploads\/sites\/154\/2020\/10\/fig6.png 687w, https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-content\/uploads\/sites\/154\/2020\/10\/fig6-300x225.png 300w\" sizes=\"auto, (max-width: 687px) 100vw, 687px\" \/><figcaption><strong>Figure 6<\/strong>\u00a0A\u00a0volume map\u00a0displayed at different contour levels. At higher contours, the volume is restricted to smaller regions of high density. It is not necessarily clear which is the &#8220;correct&#8221; contour level. Figure prepared with UCSF Chimera.<\/figcaption><\/figure><\/div>\n\n\n\n<h3 class=\"wp-block-heading\">Noise removal<\/h3>\n\n\n\n<p>Maps often contain many small peaks arising from noise in the data, which can confuse interpretation. These can be removed by &#8220;dusting&#8221;, i.e. by removing disconnected volumes smaller than a given cutoff. It may also be useful to hide dust in difference maps, in order to focus on major changes in the volume data.<\/p>\n\n\n\n<div class=\"wp-block-image\"><figure class=\"aligncenter size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"684\" height=\"343\" src=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-content\/uploads\/sites\/154\/2020\/10\/fig7.png\" alt=\"\" class=\"wp-image-188\" srcset=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-content\/uploads\/sites\/154\/2020\/10\/fig7.png 684w, https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-content\/uploads\/sites\/154\/2020\/10\/fig7-300x150.png 300w\" sizes=\"auto, (max-width: 684px) 100vw, 684px\" \/><figcaption><strong>Figure 7<\/strong>&nbsp;An example volume, before and after hiding dust. Figure prepared with UCSF Chimera.<\/figcaption><\/figure><\/div>\n","protected":false},"excerpt":{"rendered":"<p>When preparing to match two volumes from different sources, there are a number of&nbsp;pre-processing&nbsp;steps that help the comparison: Bandpass&nbsp;filtering The resolution range of the higher resolution volume will typically be restricted to that of the lower resolution volume, since the higher resolution information cannot be matched. Background peak The distribution of density values in the&#8230;<\/p>\n","protected":false},"author":6,"featured_media":0,"parent":0,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-98","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-json\/wp\/v2\/pages\/98","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-json\/wp\/v2\/comments?post=98"}],"version-history":[{"count":5,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-json\/wp\/v2\/pages\/98\/revisions"}],"predecessor-version":[{"id":222,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-json\/wp\/v2\/pages\/98\/revisions\/222"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/structural-volume-data\/wp-json\/wp\/v2\/media?parent=98"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}