model5 after conversion
- to allatom {{ task.remd_model5|linebreaks }}
+
model5
+ {% if not task.damino %}
+ after conversion to allatom
+ {% endif %}
+ {{ task.remd_model5|linebreaks }}
NGL viewer
@@ -729,6 +782,8 @@ Created {{ task.created_date }}
{% endif %}
+
Download
@@ -776,6 +831,15 @@ function display_model(numstr){
}),
stage.loadFile(
"/myfiles/download-file/{{task.jobdirname}}/MODEL"+numstr+".pdb",{defaultRepresentation: false}) .then( function( o ){
+ {% if task.damino %}
+ o.addRepresentation( "licorice",{ name: "unres", color:
+ "residueindex",colorScale:["blue","cyan", "green",
+ "yellow","orange", "red"], sele:".CA"
+ })
+ o.addRepresentation( "licorice",{ name: "unressc", visible: false, color:
+ "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
+ , sele:"*" })
+ {% else %}
o.addRepresentation( "cartoon",{ name: "unres", color:
"residueindex",colorScale:["blue","cyan", "green",
"yellow","orange", "red"]
@@ -783,10 +847,11 @@ function display_model(numstr){
o.addRepresentation( "line",{ name: "unressc", visible: false, color:
"residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
, sele:"not hydrogen and sidechainAttached" })
+ {% endif %}
return o
})
]).then(function (ol1) {
- ol1[ 0 ].superpose(ol1[ 1 ], false, ".CA")
+ ol1[ 1 ].superpose(ol1[ 0 ], false, ".CA")
ol1[ 0 ].autoView()
})
var ref=true;
@@ -824,6 +889,15 @@ function display_model(numstr){
var stage = new NGL.Stage("viewport_M"+numstr);
stage.setParameters( { backgroundColor: "white",fogFar: 60, fogNear: 45 } );
stage.loadFile( "/myfiles/download-file/{{task.jobdirname}}/MODEL"+numstr+".pdb",{defaultRepresentation: false}) .then( function( o ){
+ {% if task.damino %}
+ o.addRepresentation( "licorice",{ name: "unres", color:
+ "residueindex",colorScale:["blue","cyan", "green",
+ "yellow","orange", "red"],sele:".CA"
+ });
+ o.addRepresentation( "licorice",{ name: "unressc", visible: false, color:
+ "residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
+ , sele:"*" });
+ {% else %}
o.addRepresentation( "cartoon",{ name: "unres", color:
"residueindex",colorScale:["blue","cyan", "green",
"yellow","orange", "red"]
@@ -831,6 +905,7 @@ function display_model(numstr){
o.addRepresentation( "line",{ name: "unressc", visible: false, color:
"residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
, sele:"not hydrogen and sidechainAttached" });
+ {% endif %}
o.autoView();
})
var toggleSidechains =document.getElementById("toggleSidechainsM"+numstr );
@@ -931,6 +1006,74 @@ window.addEventListener("resize",
stage.handleResize();
},false);
+var stage_unres = new NGL.Stage("viewport_unres");
+stage_unres.setParameters( { backgroundColor: "white" } );
+/**
+[color_Red, color_Green, color_Blue, ellipsoid_width, ellipsoid_length ]
+*/
+var resdb = { 'CYS': [1.000, 1.000, 0.000, 1.33741, 2.96868],
+ 'MET': [0.000, 1.000, 0.000, 1.36694, 3.08863],
+ 'PHE': [0.000, 0.392, 0.000, 1.48323, 3.04238],
+ 'ILE': [0.000, 1.000, 0.000, 1.44098, 3.17389],
+ 'LEU': [0.000, 1.000, 0.000, 1.51054, 2.52078],
+ 'VAL': [0.000, 1.000, 0.000, 1.42072, 2.68924],
+ 'TRP': [0.000, 0.392, 0.000, 1.23867, 3.47403],
+ 'TYR': [0.596, 0.984, 0.596, 1.23060, 3.35434],
+ 'ALA': [0.000, 1.000, 0.000, 1.23266, 1.72686],
+ 'GLY': [1.000, 1.000, 1.000, 1.24626, 1.11383],
+ 'THR': [1.000, 0.000, 1.000, 1.28674, 2.59210],
+ 'SER': [1.000, 0.000, 1.000, 1.22820, 1.68800],
+ 'GLN': [1.000, 0.000, 1.000, 1.24239, 2.22201],
+ 'ASN': [1.000, 0.000, 1.000, 1.24447, 2.24946],
+ 'GLU': [1.000, 0.000, 0.000, 1.25448, 2.05551],
+ 'ASP': [1.000, 0.000, 0.000, 1.25417, 1.77556],
+ 'HIS': [1.000, 0.000, 1.000, 1.21103, 3.02627],
+ 'ARG': [0.000, 0.000, 1.000, 1.13573, 3.25143],
+ 'LYS': [0.000, 0.000, 1.000, 1.22604, 4.50054],
+ 'PRO': [0.000, 1.000, 1.000, 1.35131, 2.20525]
+ };
+stage_unres.loadFile("/myfiles/download-file/{{task.jobdirname}}/file_GB000.pdb", {defaultRepresentation: false}).then
+ (function ( o ){
+ var shape = new NGL.Shape("shape")
+ var chain = ""
+ o.addRepresentation("licorice");
+ o.structure.eachAtom(function(atom){
+ if (atom.atomname == "CA" && atom.chainname == chain) {
+ px=CAx+(atom.x-CAx)/2;
+ py=CAy+(atom.y-CAy)/2;
+ pz=CAz+(atom.z-CAz)/2;
+ shape.addSphere([px,py,pz],[0.643, 0.933, 0.960],0.6,"p");
+ }
+ if (atom.atomname == "CA") {
+ chain= atom.chainname
+ CAx= atom.x;
+ CAy= atom.y
+ CAz= atom.z
+ }
+ if (atom.atomname == "CB") {
+ mx = (atom.x-CAx);
+ my = (atom.y-CAy);
+ mz = (atom.z-CAz);
+ norm=Math.sqrt(mx*mx+my*my+mz*mz);
+ res=atom.resname;
+ var longaxis=resdb[res][4]
+ var shortaxis=resdb[res][3]
+ mx = mx /norm*longaxis;
+ my = my /norm*longaxis;
+ mz = mz /norm*longaxis;
+ resn=res+atom.resno
+ shape.addEllipsoid([ atom.x, atom.y, atom.z ],
+ [ resdb[res][0], resdb[res][1], resdb[res][2]],
+ shortaxis, [ mx, my, mz ], [ 0, shortaxis, 0 ],resn);
+ }
+ });
+ var shapeComp = stage_unres.addComponentFromObject(shape)
+ shapeComp.addRepresentation("buffer")
+ o.autoView();
+});
+
+
+
var stage = new NGL.Stage("viewport_min");
stage.setParameters( { backgroundColor: "white" } );
Promise.all([
@@ -1066,6 +1209,7 @@ window.addEventListener("resize",
o.addRepresentation( "licorice",{ color:
"residueindex",colorScale:["blue","cyan", "green", "yellow","orange", "red"]
});
+ o.setPosition([0, 0, 100]);
o.autoView();
o.addTrajectory();
});
@@ -1091,7 +1235,7 @@ window.addEventListener("resize",
isRunning = true;
trajComp.signals.frameChanged.add(function(){
- var fnum=trajComp.trajectory.currentFrame;
+ var fnum=trajComp.trajectory.currentFrame+1;
clipRange.value = fnum;
clipRange_val.innerHTML = numberWithCommas(parseInt(clipRange.value*1));
});
@@ -1106,7 +1250,7 @@ window.addEventListener("resize",
var clipRange_val = document.getElementById( "clipRange_val" );
clipRange.oninput = function( e ){
var trajComp = stage.getComponentsByName("unres_md").list[0].trajList[0];
- trajComp.setFrame(e.target.value)
+ trajComp.setFrame(e.target.value-1)
clipRange_val.innerHTML = numberWithCommas(parseInt(e.target.value*1));
};