{"id":223,"date":"2019-03-08T00:08:47","date_gmt":"2019-03-08T00:08:47","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/agfr\/?page_id=223"},"modified":"2019-04-25T23:43:32","modified_gmt":"2019-04-25T23:43:32","slug":"documentation","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/agfr\/documentation\/","title":{"rendered":"Documentation"},"content":{"rendered":"<p class=\"last-modified\">This page was last updated on April 25th, 2019 at 11:43 pm<\/p><p><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;--awb-margin-bottom:0px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\"><div class=\"fusion-text fusion-text-1\"><h3>AutoGridFR documentation<\/h3>\n<\/div><div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-separator fusion-full-width-sep\" style=\"margin-left: auto;margin-right: auto;margin-bottom:20px;width:100%;\"><div class=\"fusion-separator-border sep-shadow\" style=\"--awb-height:20px;--awb-amount:20px;background:radial-gradient(ellipse at 50% -50% , #e0dede 0px, rgba(255, 255, 255, 0) 80%) repeat scroll 0 0 rgba(0, 0, 0, 0);background:-webkit-radial-gradient(ellipse at 50% -50% , #e0dede 0px, rgba(255, 255, 255, 0) 80%) repeat scroll 0 0 rgba(0, 0, 0, 0);background:-moz-radial-gradient(ellipse at 50% -50% , #e0dede 0px, rgba(255, 255, 255, 0) 80%) repeat scroll 0 0 rgba(0, 0, 0, 0);background:-o-radial-gradient(ellipse at 50% -50% , #e0dede 0px, rgba(255, 255, 255, 0) 80%) repeat scroll 0 0 rgba(0, 0, 0, 0);\"><\/div><\/div><div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div><div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-2 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-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-2\"><p><em>AutoGridFR<\/em> (or <em>AGFR<\/em> in short) is a software program facilitating the calculation of AutoDock4 affinity maps. It is usable from the command line of through Graphical User Interface (GUI).<\/p>\n<p>In this <a href=\"https:\/\/ccsb.scripps.edu\/agfr\/overview\/\">quick overview<\/a>\u00a0we highlight the main components of the GUI and the general workflow for preparing a target file. More detailed tutorials on using the GUI for various scenarios are available below. Examples of using the command line interface are available in the <a href=\"https:\/\/ccsb.scripps.edu\/adfr\/documentation\/\">tutorials for docking with <em>ADFR<\/em><\/a>.<\/p>\n<\/div><div class=\"fusion-text fusion-text-3\"><h3>Step-by-step tutorials<\/h3>\n<\/div><div class=\"fusion-text fusion-text-4\"><p><strong>Prerequisites<\/strong><\/p>\n<ul>\n<li>You have <a href=\"http:\/\/ccsb.scripps.edu\/adfr\/Downloads\" target=\"_blank\" rel=\"noopener\">downloaded and installed ADFRsuite-1.0<\/a><\/li>\n<li>you have downloaded and unzipped the\u00a0<a href=\"https:\/\/ccsb.scripps.edu\/agfr\/download\/551\/\">data file associated with this tutorial<\/a>.<\/li>\n<\/ul>\n<p>run <em><strong>ADFRsuite-1.0\/bin\/agfrgui<\/strong><\/em>\u00a0to start the Graphical User interface for these tutorials.<\/p>\n<\/div><div class=\"fusion-content-boxes content-boxes columns row fusion-columns-2 fusion-columns-total-7 fusion-content-boxes-1 content-boxes-clean-vertical content-left content-boxes-icon-on-top\" style=\"--awb-body-color:#ffffff;--awb-title-color:#ffffff;--awb-hover-accent-color:#494e6b;--awb-circle-hover-accent-color:#494e6b;\" data-animationOffset=\"top-into-view\"><div style=\"--awb-backgroundcolor:#9acae0;border-color:rgba(255,255,255,0);\" class=\"fusion-column content-box-column content-box-column content-box-column-1 col-lg-6 col-md-6 col-sm-6 fusion-content-box-hover content-box-column-first-in-row\"><div class=\"col content-box-wrapper content-wrapper-background link-area-box link-type-text icon-hover-animation-pulsate\" data-link=\"https:\/\/ccsb.scripps.edu\/agfr\/boxLigand\/\" data-link-target=\"_self\" data-animationOffset=\"top-into-view\"><div class=\"heading heading-with-icon icon-left\"><a class=\"heading-link\" href=\"https:\/\/ccsb.scripps.edu\/agfr\/boxLigand\/\" target=\"_self\"><div class=\"icon\"><i style=\"border-color:#ffffff;border-width:1px;background-color:#494e6b;box-sizing:content-box;height:42px;width:42px;line-height:42px;border-radius:50%;font-size:21px;\" aria-hidden=\"true\" class=\"fontawesome-icon fa-university fas circle-yes\"><\/i><\/div><h3 class=\"content-box-heading\" style=\"--h3_typography-font-size:18px;line-height:23px;\">Define a docking box based on a known ligand<\/h3><\/a><\/div><div class=\"fusion-clearfix\"><\/div><div class=\"content-container\">\n<p><img decoding=\"async\" class=\"alignleft size-medium wp-image-511\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-4-300x233.png\" alt=\"\" width=\"300\" height=\"233\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-4-200x155.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-4-300x233.png 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-4-400x310.png 400w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-4-600x465.png 600w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-4-768x596.png 768w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-4-800x621.png 800w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-4.png 968w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/p>\n<\/div><\/div><\/div><div style=\"--awb-backgroundcolor:#9acae0;border-color:rgba(255,255,255,0);\" class=\"fusion-column content-box-column content-box-column content-box-column-2 col-lg-6 col-md-6 col-sm-6 fusion-content-box-hover content-box-column-last-in-row\"><div class=\"col content-box-wrapper content-wrapper-background link-area-box link-type-text icon-hover-animation-pulsate\" data-link=\"https:\/\/ccsb.scripps.edu\/agfr\/box-fill\/\" data-link-target=\"_self\" data-animationOffset=\"top-into-view\"><div class=\"heading heading-with-icon icon-left\"><a class=\"heading-link\" href=\"https:\/\/ccsb.scripps.edu\/agfr\/box-fill\/\" target=\"_self\"><div class=\"icon\"><i style=\"border-color:#ffffff;border-width:1px;background-color:#494e6b;box-sizing:content-box;height:42px;width:42px;line-height:42px;border-radius:50%;font-size:21px;\" aria-hidden=\"true\" class=\"fontawesome-icon fa-university fas circle-yes\"><\/i><\/div><h3 class=\"content-box-heading\" style=\"--h3_typography-font-size:18px;line-height:23px;\">Define a docking box based on an AutoSite detected pocket<\/h3><\/a><\/div><div class=\"fusion-clearfix\"><\/div><div class=\"content-container\">\n<p><img decoding=\"async\" class=\"alignleft size-medium wp-image-518\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-9-300x230.png\" alt=\"\" width=\"300\" height=\"230\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-9-200x153.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-9-300x230.png 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-9-400x307.png 400w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-9-600x460.png 600w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-9-768x589.png 768w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-9-800x614.png 800w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-9.png 906w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/p>\n<\/div><\/div><\/div><div style=\"--awb-backgroundcolor:#9acae0;border-color:rgba(255,255,255,0);\" class=\"fusion-column content-box-column content-box-column content-box-column-3 col-lg-6 col-md-6 col-sm-6 fusion-content-box-hover content-box-column-first-in-row\"><div class=\"col content-box-wrapper content-wrapper-background link-area-box link-type-text icon-hover-animation-pulsate\" data-link=\"https:\/\/ccsb.scripps.edu\/agfr\/box-active-site-residues\/\" data-link-target=\"_self\" data-animationOffset=\"top-into-view\"><div class=\"heading heading-with-icon icon-left\"><a class=\"heading-link\" href=\"https:\/\/ccsb.scripps.edu\/agfr\/box-active-site-residues\/\" target=\"_self\"><div class=\"icon\"><i style=\"border-color:#ffffff;border-width:1px;background-color:#494e6b;box-sizing:content-box;height:42px;width:42px;line-height:42px;border-radius:50%;font-size:21px;\" aria-hidden=\"true\" class=\"fontawesome-icon fa-university fas circle-yes\"><\/i><\/div><h3 class=\"content-box-heading\" style=\"--h3_typography-font-size:18px;line-height:23px;\">Define a docking box based receptor side chains<\/h3><\/a><\/div><div class=\"fusion-clearfix\"><\/div><div class=\"content-container\">\n<p><img decoding=\"async\" class=\"alignleft size-medium wp-image-579\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-25-300x207.png\" alt=\"\" width=\"300\" height=\"207\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-25-200x138.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-25-300x207.png 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-25-400x277.png 400w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-25-600x415.png 600w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-25-768x531.png 768w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-25-800x553.png 800w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-25-1024x708.png 1024w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-25.png 1137w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/p>\n<\/div><\/div><\/div><div style=\"--awb-backgroundcolor:#9acae0;border-color:rgba(255,255,255,0);\" class=\"fusion-column content-box-column content-box-column content-box-column-4 col-lg-6 col-md-6 col-sm-6 fusion-content-box-hover content-box-column-last-in-row\"><div class=\"col content-box-wrapper content-wrapper-background link-area-box link-type-text icon-hover-animation-pulsate\" data-link=\"https:\/\/ccsb.scripps.edu\/agfr\/flexible-receptor-sidechains\/\" data-link-target=\"_self\" data-animationOffset=\"top-into-view\"><div class=\"heading heading-with-icon icon-left\"><a class=\"heading-link\" href=\"https:\/\/ccsb.scripps.edu\/agfr\/flexible-receptor-sidechains\/\" target=\"_self\"><div class=\"icon\"><i style=\"border-color:#ffffff;border-width:1px;background-color:#494e6b;box-sizing:content-box;height:42px;width:42px;line-height:42px;border-radius:50%;font-size:21px;\" aria-hidden=\"true\" class=\"fontawesome-icon fa-university fas circle-yes\"><\/i><\/div><h3 class=\"content-box-heading\" style=\"--h3_typography-font-size:18px;line-height:23px;\">Affinity maps for docking with flexible receptor side chains<\/h3><\/a><\/div><div class=\"fusion-clearfix\"><\/div><div class=\"content-container\">\n<p><img decoding=\"async\" class=\"alignleft size-medium wp-image-568\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-18-300x224.png\" alt=\"\" width=\"300\" height=\"224\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-18-200x150.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-18-300x224.png 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-18-400x299.png 400w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-18-600x449.png 600w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-18.png 729w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/p>\n<\/div><\/div><\/div><div style=\"--awb-backgroundcolor:#9acae0;border-color:rgba(255,255,255,0);\" class=\"fusion-column content-box-column content-box-column content-box-column-5 col-lg-6 col-md-6 col-sm-6 fusion-content-box-hover content-box-column-first-in-row\"><div class=\"col content-box-wrapper content-wrapper-background link-area-box link-type-text icon-hover-animation-pulsate\" data-link=\"https:\/\/ccsb.scripps.edu\/agfr\/covalent-docking\/\" data-link-target=\"_self\" data-animationOffset=\"top-into-view\"><div class=\"heading heading-with-icon icon-left\"><a class=\"heading-link\" href=\"https:\/\/ccsb.scripps.edu\/agfr\/covalent-docking\/\" target=\"_self\"><div class=\"icon\"><i style=\"border-color:#ffffff;border-width:1px;background-color:#494e6b;box-sizing:content-box;height:42px;width:42px;line-height:42px;border-radius:50%;font-size:21px;\" aria-hidden=\"true\" class=\"fontawesome-icon fa-university fas circle-yes\"><\/i><\/div><h3 class=\"content-box-heading\" style=\"--h3_typography-font-size:18px;line-height:23px;\">Affinity maps for covalent docking<\/h3><\/a><\/div><div class=\"fusion-clearfix\"><\/div><div class=\"content-container\">\n<p><img decoding=\"async\" class=\"alignleft size-medium wp-image-511\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-4-300x233.png\" alt=\"\" width=\"300\" height=\"233\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-4-200x155.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-4-300x233.png 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-4-400x310.png 400w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-4-600x465.png 600w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-4-768x596.png 768w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-4-800x621.png 800w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-4.png 968w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/p>\n<\/div><\/div><\/div><div style=\"--awb-backgroundcolor:#9acae0;border-color:rgba(255,255,255,0);\" class=\"fusion-column content-box-column content-box-column content-box-column-6 col-lg-6 col-md-6 col-sm-6 fusion-content-box-hover content-box-column-last-in-row\"><div class=\"col content-box-wrapper content-wrapper-background link-area-box link-type-text icon-hover-animation-pulsate\" data-link=\"https:\/\/ccsb.scripps.edu\/agfr\/map-viz\/\" data-link-target=\"_self\" data-animationOffset=\"top-into-view\"><div class=\"heading heading-with-icon icon-left\"><a class=\"heading-link\" href=\"https:\/\/ccsb.scripps.edu\/agfr\/map-viz\/\" target=\"_self\"><div class=\"icon\"><i style=\"border-color:#ffffff;border-width:1px;background-color:#494e6b;box-sizing:content-box;height:42px;width:42px;line-height:42px;border-radius:50%;font-size:21px;\" aria-hidden=\"true\" class=\"fontawesome-icon fa-university fas circle-yes\"><\/i><\/div><h3 class=\"content-box-heading\" style=\"--h3_typography-font-size:18px;line-height:23px;\">Visualizing maps<\/h3><\/a><\/div><div class=\"fusion-clearfix\"><\/div><div class=\"content-container\">\n<p><img decoding=\"async\" class=\"alignleft size-medium wp-image-641\" src=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-46-300x221.png\" alt=\"\" width=\"300\" height=\"221\" srcset=\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-46-200x147.png 200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-46-300x221.png 300w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-46-400x294.png 400w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-46-600x442.png 600w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-46-768x565.png 768w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-46-800x589.png 800w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-46-1024x754.png 1024w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-46-1200x883.png 1200w, https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-46.png 1228w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/p>\n<\/div><\/div><\/div><div style=\"--awb-backgroundcolor:#9acae0;border-color:rgba(255,255,255,0);\" class=\"fusion-column content-box-column content-box-column content-box-column-7 col-lg-6 col-md-6 col-sm-6 fusion-content-box-hover content-box-column-first-in-row content-box-column-last\"><div class=\"col content-box-wrapper content-wrapper-background link-area-box link-type-text icon-hover-animation-pulsate\" data-link=\"https:\/\/ccsb.scripps.edu\/agfr\/appendix\/\" data-link-target=\"_self\" data-animationOffset=\"top-into-view\"><div class=\"heading heading-with-icon icon-left\"><a class=\"heading-link\" href=\"https:\/\/ccsb.scripps.edu\/agfr\/appendix\/\" target=\"_self\"><div class=\"icon\"><i style=\"border-color:#ffffff;border-width:1px;background-color:#494e6b;box-sizing:content-box;height:42px;width:42px;line-height:42px;border-radius:50%;font-size:21px;\" aria-hidden=\"true\" class=\"fontawesome-icon fa-university fas circle-yes\"><\/i><\/div><h3 class=\"content-box-heading\" style=\"--h3_typography-font-size:18px;line-height:23px;\">Appendix<\/h3><\/a><\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/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-bg-size:cover;width:50%;width:calc(50% - ( ( 4% ) * 0.5 ) );\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\"><div class=\"fusion-title title fusion-title-1 fusion-sep-none fusion-title-text fusion-title-size-one\" style=\"--awb-margin-top-small:10px;--awb-margin-right-small:0px;--awb-margin-bottom-small:10px;--awb-margin-left-small:0px;\"><h1 class=\"fusion-title-heading title-heading-left\" style=\"margin:0;\"><h3 style=\"text-align: center;\">FAQ<\/h3><\/h1><\/div><style type=\"text\/css\">#accordian-1 .fusion-panel:hover,#accordian-1 .fusion-panel.hover{ background-color: #f9f9f9 } #accordian-1 .fusion-panel { border-color:#494e6b; border-width:1px; background-color:#494e6b; }.fusion-accordian #accordian-1 .panel-title a .fa-fusion-box:before{ font-size: 13px;width: 13px;}.fusion-accordian #accordian-1 .panel-title a .fa-fusion-box{ color: #000000;}.fusion-accordian  #accordian-1 .panel-title a{font-family:\"Montserrat\";font-style:normal;font-weight:400;}.fusion-accordian  #accordian-1 .panel-title a:not(:hover){}.fusion-accordian  #accordian-1 .toggle-content{font-family:\"Hind\";font-style:normal;font-weight:400;}.fusion-accordian #accordian-1 .fa-fusion-box { background-color: #e91e63 !important;border-color: #e91e63 !important;}.fusion-accordian #accordian-1 .panel-title a:hover,.fusion-accordian #accordian-1 .panel-title a.hover { color: #337d93;}.fusion-faq-shortcode .fusion-accordian #accordian-1 .fusion-toggle-boxed-mode:hover .panel-title a { color: #337d93;}.fusion-accordian #accordian-1 .panel-title .active .fa-fusion-box,.fusion-accordian #accordian-1 .panel-title a:hover .fa-fusion-box,.fusion-accordian #accordian-1 .panel-title a.hover .fa-fusion-box { background-color: #337d93!important;border-color: #337d93!important;}<\/style><div class=\"fusion-faq-shortcode\" style=\"\"><ul role=\"menu\" class=\"fusion-filters clearfix\"><li role=\"presentation\" class=\"fusion-filter fusion-active\"><a role=\"menuitem\" data-filter=\".general-information\" href=\"#\">General Information<\/a><\/li><\/ul><div class=\"fusion-faqs-wrapper\"><div class=\"accordian fusion-accordian\"><div class=\"panel-group \" id=\"accordian-1\"><div class=\"fusion-panel fusion-toggle-no-divider fusion-toggle-boxed-mode panel-default fusion-faq-post fusion-faq-post-769 general-information \"><span class=\"entry-title rich-snippet-hidden\">How can I inspect a target file<\/span><span class=\"vcard rich-snippet-hidden\"><span class=\"fn\"><a href=\"https:\/\/ccsb.scripps.edu\/agfr\/author\/mgl-admin\/\" title=\"Posts by mgl-admin\" rel=\"author\">mgl-admin<\/a><\/span><\/span><span class=\"updated rich-snippet-hidden\">2019-04-15T20:03:03+00:00<\/span><div class=\"panel-heading\"><h4 id=\"faq_1-769\" class=\"panel-title toggle\"><a data-toggle=\"collapse\" class=\"collapsed\" data-parent=\"#accordian-1\" data-target=\"#collapse-1-769\" href=\"#collapse-1-769\" aria-expanded=\"false\"><div class=\"fusion-toggle-icon-wrapper\"><div class=\"fusion-toggle-icon-wrapper-main\"><div class=\"fusion-toggle-icon-wrapper-sub\"><i class=\"fa-fusion-box active-icon awb-icon-minus\" aria-hidden=\"true\"><\/i><i class=\"fa-fusion-box inactive-icon awb-icon-plus\" aria-hidden=\"true\"><\/i><\/div><\/div><\/div><div class=\"fusion-toggle-heading\">How can I inspect a target file<\/div><\/a><\/h4><\/div><div id=\"collapse-1-769\" aria-labelledby=\"faq_1-769\" class=\"panel-collapse collapse\"><div class=\"panel-body toggle-content post-content\"><p>Target files can be inspected visually using AutoDockSuite-$VERSION\/bin\/agfrgui. Alternatively AutoDockSuite-$VERSION\/bin\/about can be used to display the meta-data associate with a target file as shown below.<\/p>\n<pre>&gt; about NativeCDK2BindingSite_rigid.trg\r\ndocking target file\r\ndate : Mon Jan 28 18:54:17 2019\r\nnode : fiji\r\nplatform : Darwin-17.7.0-x86_64-i386-64bit\r\n\r\nreceptor : 4EK3_rec.pdbqt\r\nFlexRec : None\r\ncovBond : No\r\n\r\nbox : \r\ncenter : 23.332 28.922 29.598\r\nlength : 17.250 16.500 12.000\r\nsize : 0046 0044 0032\r\nspacing : 0.375\r\n\r\nmaps : C A e d OA Br NA HD N W \r\npocketMode : ['user', 23.332000000000001, 28.922000000000001, 29.597999999999999, 17.25, 16.5, 12.0]\r\n#fillpts : 247 points\r\nfile : NativeCDK2BindingSite_rigid\/translationPoints.npy\r\n&gt;<\/pre>\n<\/div><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div><\/p>\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-223","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/pages\/223","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/comments?post=223"}],"version-history":[{"count":23,"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/pages\/223\/revisions"}],"predecessor-version":[{"id":799,"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/pages\/223\/revisions\/799"}],"wp:attachment":[{"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/media?parent=223"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}