{"id":311,"date":"2019-06-06T18:43:00","date_gmt":"2019-06-06T18:43:00","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/illustrate\/?page_id=311"},"modified":"2019-06-19T14:44:07","modified_gmt":"2019-06-19T14:44:07","slug":"webdocumentation","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/illustrate\/webdocumentation\/","title":{"rendered":"Web Documentation"},"content":{"rendered":"<div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-1 nonhundred-percent-fullwidth non-hundred-percent-height-scrolling\" style=\"--awb-border-radius-top-left:0px;--awb-border-radius-top-right:0px;--awb-border-radius-bottom-right:0px;--awb-border-radius-bottom-left:0px;--awb-flex-wrap:wrap;\" ><div class=\"fusion-builder-row fusion-row\"><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-0 fusion_builder_column_1_1 1_1 fusion-one-full fusion-column-first fusion-column-last\" style=\"--awb-bg-size:cover;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\"><div class=\"fusion-clearfix\"><\/div><\/div><\/div><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-1 fusion_builder_column_1_2 1_2 fusion-one-half fusion-column-first\" style=\"--awb-bg-size:cover;width:50%;width:calc(50% - ( ( 4% ) * 0.5 ) );margin-right: 4%;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\"><div class=\"fusion-text fusion-text-1\"><h3>Options<\/h3>\n<p><strong>PDB files<\/strong><\/p>\n<p><span style=\"font-weight: 400;\">\u201cBrowse\u201d will allow you to upload a file from your computer<\/span><\/p>\n<p><span style=\"font-weight: 400;\">\u201cuse PDB id\u201d will fetch an entry from the PDB archive<\/span><\/p>\n<p><span style=\"font-weight: 400;\">\u201cProject name\u201d allows you to control the names of files that are generated<\/span><\/p>\n<p><span style=\"font-weight: 400;\">\u201cAdvanced\u201d options allow display of waters and\/or hydrogens (which are omitted by default),\u00a0<\/span><span style=\"font-weight: 400;\">as well as access to shadowing and outlining parameters<\/span><\/p>\n<p><strong>Scale Factor<\/strong><\/p>\n<p><span style=\"font-weight: 400;\">\u201cPixel per Angstrom\u201d is the scale factor used to create the illustration<\/span><\/p>\n<p><strong>Styles<\/strong><\/p>\n<p><span style=\"font-weight: 400;\">\u201cStyle\u201d provides several default display styles. These include:<\/span><\/p>\n<ul>\n<li><span style=\"font-weight: 400;\"><strong>Protein\/DNA<\/strong>&#8211;proteins in blue, DNA\/RNA in red, and heteroatoms in green<\/span><\/li>\n<li><span style=\"font-weight: 400;\"><strong>Entity\/Chain<\/strong>&#8211;uses <a href=\"http:\/\/tools.medialab.sciences-po.fr\/iwanthue\/\">IWantHue<\/a> to assign different colors to subunits<\/span><\/li>\n<li><span style=\"font-weight: 400;\"><strong>Atomic<\/strong>&#8211;modified atomic coloring, with charged oxygen\/nitrogen in saturated red\/blue,<\/span><span style=\"font-weight: 400;\">\u00a0and polar oxygen\/nitrogen in pastel colors<\/span><\/li>\n<li><span style=\"font-weight: 400;\"><strong>CPK<\/strong>&#8211;traditional atomic colors<\/span><\/li>\n<li><span style=\"font-weight: 400;\"><strong>One color<\/strong>&#8211;user defined color used for all atoms<\/span><\/li>\n<li><span style=\"font-weight: 400;\"><strong>One color range<\/strong>&#8211;user defined color, with carbon atoms slightly lighter than other atoms<\/span><\/li>\n<li><span style=\"font-weight: 400;\"><strong>Coarse<\/strong>&#8211;large spheres used for alpha carbons and two atoms in nucleic acids,\u00a0<\/span><span style=\"font-weight: 400;\">using a protein\/DNA coloring scheme<\/span><\/li>\n<li><span style=\"font-weight: 400;\"><strong>Generic<\/strong>&#8211;just outlines, for use in CellPAINT<\/span><\/li>\n<li><span style=\"font-weight: 400;\"><strong>Advanced<\/strong>&#8211;prototype method for user-defined selections, each with a given color. <\/span><span style=\"font-weight: 400;\">The three boxes are atom names, residue names, and chain ID.<\/span><\/li>\n<\/ul>\n<p><strong>Customizing Scripts<\/strong><\/p>\n<p><span style=\"font-weight: 400;\">\u201cPREVIEW INPUT TXT\u201d displays the Illustrate script in an editable window.<\/span><\/p>\n<p><span style=\"font-weight: 400;\">If you make manual changes, click on the \u201cUse Input Script\u201d box to use it for illustration.<\/span><\/p>\n<p><span style=\"font-weight: 400;\">Note: if you use this script, subsequent changes in the NGL window will not be applied.<\/span><\/p>\n<p><span style=\"font-weight: 400;\">Additional buttons will clear this script and allow uploading of external scripts.<\/span><\/p>\n<p><strong>Creating the Illustration<\/strong><\/p>\n<p><span style=\"font-weight: 400;\">\u201cAssembly\u201d and \u201cModelID\u201d buttons allow choice of different types of biological assemblies and different models. When you read in a PDB file, checkboxes will also appear for the different chains in the PDB entry&#8211;make sure that at least one is checked. The \u201cSelection\u201d box shows the current selection.<\/span><\/p>\n<p><span style=\"font-weight: 400;\">\u201cILLUSTRATE\u201d launches the Illustrate program. The time to calculate the image will be proportional to the number of atoms and also the scale factor.<\/span><\/p>\n<\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-2 fusion_builder_column_1_2 1_2 fusion-one-half fusion-column-last\" style=\"--awb-padding-top:5%;--awb-padding-right:5%;--awb-padding-bottom:5%;--awb-padding-left:5%;--awb-bg-size:cover;--awb-border-color:#000000;--awb-border-top:2px;--awb-border-right:2px;--awb-border-bottom:2px;--awb-border-left:2px;--awb-border-style:solid;width:50%;width:calc(50% - ( ( 4% ) * 0.5 ) );\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\"><div class=\"fusion-text fusion-text-2\"><p><span style=\"font-weight: 400;\">The website is designed to allow quick access to several useful representations, and options for customizing representations as you become more familiar with the method.<\/span><\/p>\n<h3><strong>To get started:<\/strong><\/h3>\n<p><span style=\"font-weight: 400;\">1) type a PDB id in the \u201cuse PDB id\u201d box<\/span><\/p>\n<p><span style=\"font-weight: 400;\">2) choose one of the options in \u201cStyle\u201d<\/span><\/p>\n<p><span style=\"font-weight: 400;\">3) orient the molecule in the NGL window<\/span><\/p>\n<p><span style=\"font-weight: 400;\">4) click on \u201cILLUSTRATE\u201d<\/span><\/p>\n<p><span style=\"font-weight: 400;\">5) when the image appears, you can save it by right-click on the image<\/span><\/p>\n<\/div><div class=\"fusion-text fusion-text-3\"><h3><span style=\"font-weight: 400;\">Warnings!<\/span><\/h3>\n<p><span style=\"font-weight: 400;\">Biological molecules, and the ways that scientists study them, are immensely diverse and complex, so it is difficult to find defaults that work for everything. A few places that you might encounter problems include:<\/span><\/p>\n<p><span style=\"font-weight: 400;\">1) very large molecules may not fit within the maximum image size of 3000X3000 pixels. If this happens, try a smaller \u201cPixel per Angstrom\u201d scale size.<\/span><\/p>\n<p>2) HETATMs are used in several ways in PDB entries, including free ligands and substrates and modified amino acids and nucleotides in chains. You may have to tweak the script manually to get the results you want.<\/p>\n<\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-311","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ccsb.scripps.edu\/illustrate\/wp-json\/wp\/v2\/pages\/311","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ccsb.scripps.edu\/illustrate\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ccsb.scripps.edu\/illustrate\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/illustrate\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/illustrate\/wp-json\/wp\/v2\/comments?post=311"}],"version-history":[{"count":18,"href":"https:\/\/ccsb.scripps.edu\/illustrate\/wp-json\/wp\/v2\/pages\/311\/revisions"}],"predecessor-version":[{"id":356,"href":"https:\/\/ccsb.scripps.edu\/illustrate\/wp-json\/wp\/v2\/pages\/311\/revisions\/356"}],"wp:attachment":[{"href":"https:\/\/ccsb.scripps.edu\/illustrate\/wp-json\/wp\/v2\/media?parent=311"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}