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<!DOCTYPE HTML><meta http-equiv="content-type" content="text/html; charset=UTF-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="theme-color" content="#377"><meta name="viewport" content="width=device-width,initial-scale=1.0,minimum-scale=1.0,maximum-scale=1.0,user-scalable=no"><title>YorodumiPrime - PDB-2ht7</title><link rel="icon" href="img/lk-prime.gif"><script src="//code.jquery.com/jquery-3.4.1.min.js"></script><script>molmil_settings={src:'//gjbekker.github.io/molmil/'};</script><script src="//gjbekker.github.io/molmil/molmil.js"></script><style> :root{--col-dark:#377;--col-medium:#8bb;--col-bright:#dee;}html,body{height:100%;}button{font-size:medium}button img,button{vertical-align:middle}button,a,select,label,.lk,.clickable{cursor:pointer}.clickable:hover{color:blue;}li{margin:0.3em 0 0.3em 1em;padding:0}p{margin:0.3em 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soup)},postjob:function(){_mm.style_init();_mm.rebuild();_popvw.set_ready()}}; var _mm={mmname:{},ui:null,init:function(){this.mmname={color:{grp:molmil.colorEntry_Group,cpk:molmil.colorEntry_CPK,str:molmil.colorEntry_Structure},style:{hide:molmil.displayMode_None,defo:molmil.displayMode_Default,cartoon:molmil.displayMode_Cartoon,bs:molmil.displayMode_BallStick,stk:molmil.displayMode_Stick,cpk:molmil.displayMode_Spacefill}};this.ui=new molmil.UI(soup);return this},one_seq:{},resname2one:{"ALA":"A","CYS":"C","ASP":"D","GLU":"E","PHE":"F","GLY":"G","HIS":"H","ILE":"I","LYS":"K", "LEU":"L","MET":"M","ASN":"N","PRO":"P","GLN":"Q","ARG":"R","SER":"S","THR":"T","VAL":"V","TRP":"W","TYR":"Y","DA":"A","DT":"T","DG":"G","DC":"C","A":"A","T":"T","U":"U","G":"G","C":"C","PSU":"U","MSE":"M","UNK":"X"},ccol:{"A":[154,166,204,1],"B":[141,204,141,1],"C":[204,154,160,1],"D":[204,204,102,1],"E":[204,154,204,1],"F":[141,192,192,1],"G":[204,166,90,1],"H":[192,102,102,1],"I":[196,178,143,1],"J":[0,153,204,1],"K":[164,74,74,1],"L":[82,164,136,1],"M":[123,164,40,1],"N":[190,104,190,1],"O":[0, 165,167,1],"P":[0,204,102,1],"Q":[48,143,90,1],"R":[0,0,111,1],"S":[151,146,86,1],"T":[0,80,0,1],"U":[102,0,0,1],"V":[102,102,0,1],"W":[102,0,102,1],"X":[0,102,102,1],"Y":[147,107,9,1],"Z":[142,27,27,1],"0":[0,204,102,1],"1":[48,143,90,1],"2":[0,0,111,1],"3":[151,146,86,1],"4":[0,80,0,1],"5":[102,0,0,1],"6":[102,102,0,1],"7":[102,0,102,1],"8":[0,102,102,1],"9":[147,107,9,1]},selection:null,select:function(cmd,param){if(typeof cmd=="string")this.selection=molmil.quickSelect(cmd,soup);else this.selection= cmd;return this},selected:function(mode){return this.selection||soup.structures[0]},select_chain:function(chains){var atm=[],mol=[];if(typeof chains==="string")chains=[chains];soup.structures[0].chains.forEach(function(c){if(chains.indexOf(c.name)==-1)return;c.molecules.forEach(function(c2){atm=atm.concat(c2.atoms);mol.push(c2)})});this.selection={atoms:atm,molecules:mol};return this},select_res:function(inobj){var atm=[],mol=[],res_in_chain;console.log(inobj);soup.structures[0].chains.forEach(function(c){if(!inobj[c.name])return; res_in_chain=inobj[c.name].map(function(v){return parseInt(v)});c.molecules.forEach(function(c2){if(res_in_chain.indexOf(c2.id)==-1)return;atm=atm.concat(c2.atoms);mol.push(c2)})});this.selection={atoms:atm,molecules:mol};return this},select_seq:function(asid,seq){var atm=[],mol=[],tg_chain,matchres={},m=0;soup.structures[0].chains.forEach(function(c){if(c.name!=asid)return;tg_chain=c.molecules});if(!tg_chain){_popvw.cmdhist("no chain: "+asid);return this}if(!this.one_seq[asid]){this.one_seq[asid]= "";tg_chain.forEach(function(r){this.one_seq[asid]+=this.resname2one[r.name]||"X"}.bind(this))}while(true){m=this.one_seq[asid].indexOf(seq.toUpperCase(),m);if(m==-1)break;for(i=m;i<m+seq.length;i++)matchres[i]=true;++m}Object.keys(matchres).forEach(function(n){atm=atm.concat(tg_chain[n].atoms);mol.push(tg_chain[n])});this.selection={atoms:atm,molecules:mol};return this},style_init:function(only){var do_style=only!="color";var do_color=only!="style";this.select();if(phpvar.ent.db=="pdb"){if(do_style){this.style("defo").style("ligand_style"); this.select("resn HOH").color("cpk").style("hide").select()}if(do_color){if(phpvar.initstyle.multic)this.color("jmolchain");else this.color("grp");this.style("ligand_color")}}else if(phpvar.ent.db=="chem"){if(do_style)this.style("bs");if(do_color)this.color("cpk")}else if(phpvar.ent.db=="sasbdb"||phpvar.ent.db=="sasbdb-model")if(phpvar.initstyle.dummy){if(do_style)this.style("cpk");if(do_color)this.color("cpk")}else{if(do_style)this.style("defo");if(do_color)this.color("jmolchain")}phpvar.init_cmd&& eval(phpvar.init_cmd);return this},color:function(mode){if(typeof mode!="string")molmil.colorEntry(this.selected(),molmil.colorEntry_Custom,mode);else if(mode=="jmolchain"){var that=this;this.selected().chains.forEach(function(c){if(c.isHet||c.molecules[0].name=="HOH")return;var cn=c.authName||c.name||"A";molmil.colorEntry(c,molmil.colorEntry_Custom,that.ccol[cn.substring(cn.length-1).toUpperCase()])})}else if(mode=="init")this.style_init("color");else molmil.colorEntry(this.selected(),this.mmname.color[mode]); return this},style:function(mode){if(mode=="ligand_color")this.selected().chains.forEach(function(c){if(!c.isHet)return;molmil.colorEntry(c,molmil.colorEntry_CPK)});else if(mode=="ligand_style")this.selected().chains.forEach(function(c){if(!c.isHet)return;if(c.atoms&&c.atoms.length==1)molmil.displayEntry(c,molmil.displayMode_BallStick);else molmil.displayEntry(c,molmil.displayMode_Stick)});else if(mode=="init")this.style_init("style");else molmil.displayEntry(this.selected(),this.mmname.style[mode|| "defo"]);return this},show_sidechain:function(flg){var colatoms=[];molmil.displayEntry(_mm.selection.molecules,molmil.displayMode_Stick_SC);_mm.selection.atoms.forEach(function(c){if(c.element=="C")return;colatoms.push(c)});molmil.colorEntry(colatoms,molmil.colorEntry_CPK);return this},styleset:function(mode){this.select().style(mode).rebuild();_popvw.cmdhist("Style applied")},colorset:function(mode){this.select().color(mode).rebuild();_popvw.cmdhist("Color applied")},delchain:function(t_chain){if(typeof t_chain=== "string")t_chain=[t_chain];var idxs=[];soup.structures[0].chains.forEach(function(c,i){if(t_chain.indexOf(c.name)===-1)return;idxs.unshift(i)});idxs.forEach(function(i){soup.structures[0].chains.splice(i,1)});return this},focus:function(){var sel=this.selected(),cnt;if(sel.molecules)cnt=sel.molecules.length+" residues";if(sel.atoms)sel=sel.atoms;if(!cnt)cnt=sel.length+" atoms";molmil.selectAtoms(sel,false,soup);if(sel.length==0){molmil.resetCOG(canvas,false);_popvw.cmdhist("No atom selected","red")}else{molmil.selectionFocus(soup, 1);_popvw.cmdhist("Focusing on selected "+cnt);canvas.renderer.updateSelection()}this.rebuild();return this},reset_focus:function(){canvas.molmilViewer.calculateCOG();canvas.renderer.camera.z=canvas.molmilViewer.calcZ();canvas.renderer.camera.z_set=true;molmil.selectAtoms([],false,soup);this.rebuild();canvas.update=true;return this},zoom:function(lev){canvas.renderer.camera.z=canvas.renderer.camera.z/lev;canvas.update=true;return this},reset_view:function(){canvas.renderer.camera.reset();this.reset_focus(); return this},anim:function(p){},config:function(key,val){molmil.configBox[key]=val;molmil.shaderEngine.recompile(canvas.molmilViewer.renderer);if(key==="stereoMode"){canvas.renderer.camera.z=canvas.molmilViewer.calcZ()/(val?1/2:3);canvas.renderer.camera.z_set=true;if(val)_mm.zoom(2)}canvas.update=true;return this},uiset:function(cmd,param){if(cmd=="molmil_menu"){$(".molmil_UI_LB_icon").toggle("medium");$(".molmil_UI_RB_icon").toggle("medium")}else if(cmd=="console"){this.ui.toggleCLI();_resize_canvas()}return this}, rebuild:function(){soup.renderer.initBuffers();canvas.update=true;return this},asb:function(aid,disp_mode){molmil.toggleBU(aid===undefined?-1:aid,disp_mode||4,3,soup.structures[0],soup);var str="assembly #"+aid;if(aid===undefined||aid===-1){_mm.select().rebuild();str="asymmetric unit"}_popvw.cmdhist("Displaying "+str);return this}}; var _cmd={asb:function(param,trg_obj){_mm.asb(param);trg_obj&&_ofunc("_btn_deco","asb",trg_obj)},focus_chain:function(param,trg_obj){_mm.select_chain(param).focus();trg_obj&&_ofunc("_btn_deco","select",trg_obj)},focus_res:function(param,trg_obj){_mm.select_res(param).show_sidechain().focus();trg_obj&&_ofunc("_btn_deco","select",trg_obj)},focus_res_ns:function(param,trg_obj){_mm.select_res(param).focus();trg_obj&&_ofunc("_btn_deco","select",trg_obj)},focus_seq:function(param,trg_obj){_popvw.cmdhist("Sequence: "+ param.aid+"-"+param.seq);_mm.select_seq(param.aid,param.seq).focus();trg_obj&&_ofunc("_btn_deco","select",trg_obj)},focus_reset:function(){_mm.reset_focus()},water:function(param){soup.waterToggle(param);_mm.select("resn HOH").style(param?"bs":"hide").rebuild();_popvw.cmdhist(param?"Water shown":"Water hidden")},other:function(param,trg_obj){_popvw.cmdhist("unknown command")}}; _vwui={style:function(o){_mm.select().style($(o).val()).rebuild();_popvw.cmdhist("Style applied")},color:function(o){_mm.select().color($(o).val()).rebuild();_popvw.cmdhist("Color applied")},blackbg:function(o){var ck=$(o).prop("checked");_mm.config("BGCOLOR",ck?[0,0,0,1]:[1,1,1,1]);_localstr.setbool("blackbg",ck)},fog:function(o){var ck=$(o).prop("checked");_mm.config("glsl_fog",ck);_localstr.setbool("nofog",!ck)},stereo:function(o){var ck=$(o).prop("checked");_mm.config("stereoMode",ck?1:0);_localstr.setbool("stereo", ck)}}; </script>