2.2250.0false400250400.01.3598codebase/public/part2/pnaurl/Users/btinker/Desktop/dna/page10pna_original$0.mmlsize107410filenamepage10pna_original$0.mmldate1239995975000define %success 0;transcribe the mRNA200Transcriptionshow selectionhalo off;
select atom within (%atom[60].rx, "%height-8", %width, "%atom[90].rx-%atom[60].rx");
set kelvin 3000;
select atom not selected;
set kelvin 6000;
select atom none;
if(%model_time<5000);
set %alpha 255;
set %success 0;
set %at1 -1;
set %at2 -1;
set %n 61;
set %type complementaryType(%atom[%n].id, RNA);
set %sp -1;
set image[0].x %image[0].x+1;
set image[0].y %image[0].y+1.4;
set textbox[2].x %image[0].x+2;
set textbox[2].y %image[0].y+2;
return;
endif;
if(%n>61); // move the text box to invisible
//set textbox[2].x %textbox[2].x-1; // don't slide
if(%alpha > 0);
set %alpha %alpha-10;
if(%alpha < 0);
set %alpha 0;
endif;
set textbox[2].color (0, 0, 0, %alpha);
set textbox[2].background (0, 255, 0, %alpha);
endif;
endif;
if(%n>91); // finish
attach image 0 to atom -1; // detach image
set image[0].y %image[0].y-1;
if(%image[0].y + %image[0].height < 0);
stop;
endif;
return;
endif;
if(%atom[%n].charge < 0.1);
// first search in larger distance and use electrostatic force to
// put them together
set %k nearesttoatom(%type, %n, 10, 1);
if(%k >= 0);
set atom[%n].charge 1;
set %m whichrbond(%k);
set atom[%rbond[%m].atom2].charge -2;
endif;
else;
// then narrow down the search in a closer distance and pin them down
// and move forward to the next step
set %k nearesttoatom(%type, %n, 3, 1);
if(%k>=0 and %k!=%at2);
set %m whichrbond(%k);
set %at1 %rbond[%m].atom1;
set %at2 %rbond[%m].atom2;
set %n1 %n-1;
attach image 0 to atom %n1;
select atom all;
charge 0;
select atom none;
set atom[%at1].restraint 1000;
set atom[%at2].restraint 1000;
set atom[%at1].friction 5;
set atom[%at2].friction 5;
set atom[%at1].vx 0;
set atom[%at2].vx 0;
set atom[%at1].vy 0;
set atom[%at2].vy 0;
set atom[%at1].restraint.x %atom[%n1].rx;
set atom[%at2].restraint.x %atom[%n1].rx;
set atom[%at1].restraint.y %atom[%n1].ry-3-%rbond[%m].bondlength;
set atom[%at2].restraint.y %atom[%n1].ry-3;
if(%sp == -1);
// lightly bond them so that they will be treated as a whole
bond %n %at2 0.001;
set rbond["%number_of_rbonds-1"].style GHOST_STYLE;
else;
if(%at1 != %sp);
bond %sp %at1 0.01;
set rbond["%number_of_rbonds-1"].bondlength 1.92;
endif;
endif;
set %sp %at1;
set %n %n+2;
set %type complementaryType(%atom[%n].id, RNA);
set %success 1;
else;
set atom[%at1].friction 0;
set atom[%at2].friction 0;
endif;
endif;
show selectionhalo on;
Add a nucleotide when one is bound to the template 75Add nucleotide1if(%success==0);
return;
endif;
set %oldn %number_of_atoms;
add atom 25 (1, 1);
add atom %type (1, 2.6);
if(%number_of_atoms-%oldn==0); // both failed
return;
endif;
if(%number_of_atoms-%oldn==1); // one ailed
select atom %oldn;
remove;
return;
endif;
set %oldn1 %oldn+1;
bond %oldn %oldn1 0.2;
set atom[%oldn].vx 300;
set atom[%oldn1].vx 300;
set %success 0;
204255255255Nonepolymerase.gif21-129.016.024false11falseArial Bold11560class org.concord.mw2d.models.Atom113' -1.9295687675476074223.4378356933593811falseArial Bold11590class org.concord.mw2d.models.Atom12 5'284.50189208984375224.285263061523441102550255Arial11213RNA Polymerase-132.0133.025false159.926766778542846.782527947445440.0193766724133897370.00778202603655148926false166.0647264303686460.9498574199024860.00362417857281458530.005377055667454732525false105.42917999555907113.730823194919440.023983819100093767-0.0357948530038714929false110.8084353143773596.69804788286375-0.02563481023340731-0.01995017476658876625false48.84857681887089632.76718951285271-0.02687432837859671-0.016367690683675128false43.15142318112910417.232810487147290.011438621948565335-0.01467527141081229625false320.74686302544677102.64496168019971-0.0168822753052669080.0342600241722407227false335.2531369745533109.35503831980029-0.0054354651633828420.02023923193733376625false96.02295749208186187.7712417445615-0.0297866725717151480.0037795360014729130false106.8244262193073176.822880565343720.0298927048851232030.03656910177152642625false314.6496400785791142.339503187171350.00604871826521603-0.01676329156618338826false329.3503599214208145.660496812828650.0133957614740847460.01310752340142995325false79.1951914473917977.92318678045021-0.0157898546288177-0.02849425836819644426false64.8048085526082174.076813219549820.0061055332457968580.01949230681368128325false138.450193327132198.50775124442987-0.016024701739776720.02189554313407368626false123.9205997042713196.12467861240877-0.03453140409300656-0.01373768484852297425false264.0778634862823594.88696141850653-0.015070742910188333-0.003282388348050132426false248.36443247010257100.172736964175480.005224552116114075-0.00241815062924545625false94.29334039361655149.75378508098880.018706203044829530.03770172513129660426false97.73790774091275164.585590143129680.040189536187936116-0.001362864001330701525false140.53078313224435125.04095064260173-0.0074575475764843190.0441408220940813730false141.46921686775568142.959049357398270.013392666056491040.01082413319402740825false373.084752258403581.537739189714270.0395471087766997640.01588754650749816729false364.915247741596596.46226081028570.04537834749792920.02299164415065520625false240.02088638877972.20972902749666-0.0163487604072587240.005790033301226420530false253.8338975597090284.35898919707270.00328448879812125350.0224586907929672625false224.3180464754579834.74564891224121-0.014735015971671905-0.02995753223935435427false239.6819535245420537.25435108775879-0.007053241048565504-0.00703667004156595325false323.77838923145225183.54473197309410.015315851858301326-0.01286323206189440829false323.3023018480789198.18730985527657-4.847378428446414E-40.01777047239373084225false71.56290843235894176.12555800049623-0.025822246978633750.002229309820677285328false56.43709156764106181.87444199950377-0.0055489484050063810.01622281477179129625false359.6033385918678150.320951918699250.009285566018319478-0.02768128530964982728false364.39666140813216165.67904808130078-0.02065501248535897-0.0187670032277209725false106.752824871503851.490308173187340.0103752235018379390.00910684885475978328false119.2471751284961760.50969182681268-0.0065541292469863350.0209414212417570525false165.2686619013486112.483666514256160.023039419141012485-0.024856531941002828false170.7313380986514127.516333485743840.004188637169013582-0.0635458241513057225false355.327024949042142.29777572685043-0.017430950700227765-0.01581948756042897428false366.672975050957853.70222427314957-0.010151904752089916-0.02357507330622364225false230.50516057604247106.410680160306410.04072290400644572-0.00642857731146409427false213.51168219821645110.970846119960130.028529277292692327-0.00911120117733061725false88.3991601336651915.055743845542540.015779422003168304-0.004500523427154420527false79.7238373793348129.167450677687427-0.04981097035842798-0.00908067607345045725false193.9425628029492133.407561556384020.013635797936721340.017554860924201227false211.03543941840522131.6473345064191-0.01658757557897998-0.00781482886151619125false61.05682134772417118.3914853418340.011479902622855542-0.01170759676256139327false76.94317865227583125.608514658166-0.034916112248188060.001099325476170116325false278.8301568701396635.90291225805281-0.00131153875153657480.0104566034644207627false291.169843129860348.09708774194720.0123595315253681830.0392706203758659725false329.441087939003632.794142992374090.00191799727283436540.01080558639961281230false340.558912060996425.205857007625910.026253166463293474-0.002636469098776094325false34.47294485115156135.22062844762542-0.015882417877696720.0281165991569925830false31.527055148848447120.779371552374630.0323496631286494740.003069491730842135225false189.2019531959248157.12237811215616-0.00308344351942584860.02388668442889445330false201.69235858770062167.88646852387117-0.02418040167048744-0.01161249950942312925false171.29569088433016164.0963137252878-0.0035665712699952906-3.2155428799697836E-430false171.3964104105848180.909127184949030.031882201974138740.00657024692910547825false183.377252957277912.7289988631342560.026564302789500860.02403027818457005230false199.552833884062811.426859065350751-0.0148496789271646350.00410887655542194325falsetruefalse100.057.993397683253306237.2606969552437359.07043123620859237.43784132430130.02721987713425954-0.01409492327046008927falsefalse57.81849602830818219.4183204287118-0.010223353079518264-0.02592133197107665525falsetruefalse100.077.19339163483436237.2759370094368677.76318556392616239.26019794255450.0188862824742770870.01791138632111266226falsefalse78.72804359684415223.3520193457689-0.0072189132517289790.0145574610372242525falsetruefalse100.096.39338558641538237.2911770636396.42278205743274238.46026342295167-0.03719554531965660.01600697892950929428falsefalse95.56872663295368219.465025431326950.02700939973641175-0.02788372744452572625falsetruefalse100.0115.59337953799647237.30641711782314117.12104389133181238.31568966355090.0019284978351656063-0.0360259040811279827falsefalse117.5096460651799220.48704353091350.0318555870759773540.00632744998328923625falsetruefalse100.0134.79337348957742237.32165717201627136.5506462106263238.80439077746198-0.0068657337317421230.0221700193644005127falsefalse136.20032467815625224.35360035443970.0051695153242557470.01171740288121782825falsetruefalse100.0153.99336744115848237.3368972262094155.30509409454578236.43977376782560.004265964763217083-0.02640393341268817326falsefalse155.02204338583593220.74183697800980.014251682854780458-0.0254151518126283425falsetruefalse100.0173.19336139273952237.35213728040256174.73515458308935236.870810162483820.010773224369624067-0.01345347895955128928falsefalse175.65722035798896220.865258413535680.028149572446460224-0.02036659548893989325falsetruefalse100.0192.39335534432053237.3673773345957193.22181960631391236.106261401413630.011836583699860006-0.00513967696223367326falsefalse191.93582308704316219.5707107999640.020512252772200944-0.03070526778098880325falsetruefalse100.0211.5933492959016237.38261738878882211.78541904472618236.75160533261325-0.004049390892136076-0.01876293128290398529falsefalse213.09008991354878221.707666890763250.0010035833162551574-0.002252310692566421325falsetruefalse100.0230.7933432474826237.39785744298197231.33526575420558237.19899690963790.012075658725641678-0.0077356159702753828falsefalse232.66865684842432222.10580979409290.023023783023531280.0165440987772730425falsetruefalse100.0249.9933371990636237.4130974971751250.2757119368265237.56031280112094-0.04606486650611743-0.02233749708550128829falsefalse251.42342700102805219.9788563981936-0.004638144854141163-0.02283311246614490325falsetruefalse100.0269.19333115064467237.42833755136823268.97207039655655237.89495703495467-0.0048150669756991130.0193285921222409827falsefalse269.17592281476834220.60196164872806-0.021831195302839570.03402191623850884425falsetruefalse100.0288.39332510222573237.4435776055614288.1255586692847237.477140311370140.0024740230840591590.02037189612736028628falsefalse287.84844154509096219.567949725436530.0121948097333661530.01339699666546927625falsetruefalse100.0307.5933190538068237.45881765975452307.55634029725786238.93499693478557-0.00296955432125186940.02546319147612720329falsefalse306.63033660692827222.777734000006940.010559807111898705-0.00286585673291390825falsetruefalse100.0326.79331300538774237.47405771394764327.2680007615988237.37714836149794-0.030020666056977930.0190264252544403528falsefalse326.8154891000046220.199768324792330.0118780646436381970.01348333409921385425falsetruefalse100.0345.9933069569688237.4892977681408345.50188710568364238.285255722349970.00540998083197769-0.0183771179995916529falsefalse348.25834877212003221.12888890568428-0.002677642811362861-9.469489682760571E-425false206.1951914473917859.9231867804502-0.0157898546288177-0.02849425836819644426false191.8048085526082256.076813219549810.0061055332457968580.01949230681368128325false273.1951914473918149.92318678045018-0.0157898546288177-0.02849425836819644426false258.8048085526082146.076813219549820.0061055332457968580.01949230681368128325false31.195191447391792160.92318678045018-0.0157898546288177-0.02849425836819644426false16.804808552608208157.07681321954980.0061055332457968580.0194923068136812833064116.00.22316.00.24516.00.26716.00.28916.00.2101116.00.2121316.00.2141516.00.2161716.00.2181916.00.2202116.00.2222316.00.2242516.00.2262716.00.2282916.00.2303116.00.2323316.00.2343516.00.2363716.00.2383916.00.2404116.00.2424316.00.2444516.00.2464716.00.2484916.00.2505116.00.2525316.00.2545516.00.2565716.00.2585916.00.2606116.00.2626316.80.2626019.20.2646516.80.2646219.20.2666716.80.2666419.20.2686916.80.2686619.20.2707116.80.2706819.20.2727316.80.2727019.20.2747516.80.2747219.20.2767716.80.2767419.20.2787916.80.2787619.20.2808116.80.2807819.20.2828316.80.2828019.20.2848516.80.2848219.20.2868716.80.2868419.20.2888916.80.2888619.20.2909116.80.2908819.20.2929316.00.2949516.00.2969716.00.26261601.570796326794896650.06360621.570796326794896650.06463621.570796326794896650.06562641.570796326794896650.06665641.570796326794896650.06764661.570796326794896650.06867661.570796326794896650.06966681.570796326794896650.07069681.570796326794896650.07168701.570796326794896650.07271701.570796326794896650.07370721.570796326794896650.07473721.570796326794896650.07572741.570796326794896650.07675741.570796326794896650.07774761.570796326794896650.07877761.570796326794896650.07976781.570796326794896650.08079781.570796326794896650.08178801.570796326794896650.08281801.570796326794896650.08380821.570796326794896650.08483821.570796326794896650.08582841.570796326794896650.08685841.570796326794896650.08784861.570796326794896650.08887861.570796326794896650.08986881.570796326794896650.09089881.570796326794896650.09188901.570796326794896650.0