(window.webpackJsonp=window.webpackJsonp||[]).push([[50],{506:function(e,t,i){"use strict";i.r(t);var r=i(71),o=Object(r.a)({},(function(){var e=this,t=e.$createElement,i=e._self._c||t;return i("ContentSlotsDistributor",{attrs:{"slot-key":e.$parent.slotKey}},[i("h1",{attrs:{id:"chemical-interactions"}},[i("a",{staticClass:"header-anchor",attrs:{href:"#chemical-interactions"}},[e._v("#")]),e._v(" Chemical Interactions")]),e._v(" "),i("p",[e._v("The Chemical Interactions plugin visualizes ligand-receptor and protein-protein interactions. It utilizes "),i("a",{attrs:{href:"https://github.com/PDBeurope/arpeggio",target:"_blank",rel:"noopener noreferrer"}},[e._v("arpeggio"),i("OutboundLink")],1),e._v(" for calculating interactions.")]),e._v(" "),i("h2",{attrs:{id:"instructions"}},[i("a",{staticClass:"header-anchor",attrs:{href:"#instructions"}},[e._v("#")]),e._v(" Instructions")]),e._v(" "),i("br"),e._v(" "),i("vimg",{attrs:{src:"plugins-page/chem_interactions_menu_labeled.png"}}),e._v(" "),i("ol",[i("li",[i("p",[e._v("Select Structure 1 from the dropdown. this should be the receptor, or the larger of the two interacting proteins")])]),e._v(" "),i("li",[i("p",[e._v("Set your Selection mode for Structure 2")]),e._v(" "),i("ul",[i("li",[i("strong",[e._v("Selected Atoms/Residues")]),e._v(": Uses the atoms/residues selected in the workspace, and calculates interactions with Structure 1.\n"),i("ul",[i("li",[e._v("Atoms/residues can be from any complex in the Entry List.")]),e._v(" "),i("li",[e._v("Does not require the Structure 2 dropdown")])])]),e._v(" "),i("li",[i("strong",[e._v("Specific Structures")]),e._v(": Select either another complex in the workspace, or a ligand extracted from Structue 1.\n"),i("ul",[i("li",[e._v("When Structure 1 dropdown is populated, the plugin automatically detects ligands, and adds them to the choices for Structure 2.")])])]),e._v(" "),i("li",[e._v("For performance, you want to minimize the number of atoms in your selections for Structure 2. Doing a full protein-protein calculation can cause long render times, so we advise you narrow down your selection as much as possible.")])])]),e._v(" "),i("li",[i("p",[e._v("Press Calculate, which will identify interactions using arpeggio, and render results in your workspace.")])]),e._v(" "),i("li",[i("p",[e._v("Modify the Display Settings to show or hide interactions of interest.")]),e._v(" "),i("ul",[i("li",[e._v("Change the visibility or color of each interaction type")]),e._v(" "),i("li",[i("code",[e._v("Hide All")]),e._v(": Quickly Hide all interaction lines. Toggles through "),i("em",[e._v("Hide All")]),e._v(", "),i("em",[e._v("Show All")]),e._v(", and "),i("em",[e._v("Show Default")])]),e._v(" "),i("li",[i("code",[e._v("Clear Frame")]),e._v(" button will delete all interaction lines currently visible in the workspace.")])])])])],1)}),[],!1,null,null,null);t.default=o.exports}}]);