1.5300.0false500300500.01.0122filenamepage11$0.mmldate1222442723627urlC:\home\mw\public\part2\pna\page11$0.mmlsize125738codebaseC:\home\mw\public\part2\pnaTranslate mRNA into polypeptide200Translationshow selectionhalo off;
select atom within (%atom[0].rx, "%height-8", %width, "%atom[30].rx-%atom[0].rx");
set kelvin 1000;
select atom not selected;
set kelvin 1000;
select atom none;
if(%model_time < 500);
// we do not want the charges set for the amino acid to interfere with
// our charge pulling scheme, so we neutralize every particle
select atom all;
charge 0;
select atom none;
endif;
if(%model_time<5000);
set %alpha 255;
set %stopcodon 0;
set %mol -1;
set %previous -1;
set %lastbond -1;
set %n 1;
set %n2 %n+2;
set %type complementaryType(%atom[%n].id, %atom[%n2].id, %atom[%n+4].id, PROTEIN);
set image[0].x %image[0].x+0.8;
set image[0].y %image[0].y+0.7;
set textbox[2].x %image[0].x;
set textbox[2].y %image[0].y+2;
return;
endif;
if(%model_time>6000); // dim the text box to invisible
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>48 or %stopcodon>0); // 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;
if(%lastbond>=0);
select rbond %lastbond;
remove;
set %lastbond -1;
endif;
select atom all;
damp 0;
set hx 0;
set hy 0;
set %mol whichmolecule(%k);
if(%mol>=0);
select molecule %mol;
restrain 0;
mark color 0xccffcc;
select molecule none;
endif;
select atom none;
show selectionhalo on;
return;
endif;
if(%atom[%n2].charge < 0.1);
// first search in larger distance and use electrostatic force to
// put them together
set %k nearesttoatom(%type, %n2, 10, 1);
if(%k >= 0);
set atom[%n2].charge 1;
set atom[%k].charge -1;
set atom[%n2].friction 1;
set atom[%k].friction 1;
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, %n2, 3, 1);
if(%k>=0);
if(%n2<44);
attach image 0 to atom "%n2+4";
endif;
select atom all;
charge 0;
select atom none;
set atom[%n2].friction 0;
set atom[%k].vx 0;
set atom[%k].vy 0;
set atom[%k].friction 1;
set atom[%k].restraint 100;
set atom[%k].restraint.x %atom["%n2+4"].rx;
set atom[%k].restraint.y %atom["%n2+4"].ry-2;
if(%lastbond>=0);
select rbond %lastbond;
remove;
else;
set atom[%k].hx -0.1;
set atom[%k].hy -0.1;
endif;
bond %k %n2 0.0001;
set %lastbond %number_of_rbonds-1;
set rbond[%lastbond].style GHOST_STYLE;
if(%previous>=0);
set atom[%previous].restraint 0;
bond %previous %k 0.2;
set rbond["%number_of_rbonds-1"].bondlength (%atom[%previous].sigma+%atom[%k].sigma)*0.5+0.5;
endif;
set %previous %k;
set %n %n+6;
set %n2 %n+2;
if(%n<=43);
set %type complementaryType(%atom[%n].id, %atom[%n2].id, %atom[%n+4].id, PROTEIN);
if(%type==-1); // stop codon
set %stopcodon 1;
endif;
endif;
else;
//what to do?
endif;
endif;
show selectionhalo on;204255255255Noneribosome.gif28-95.0000051409007126.0000047385693425519212825542.02055.0425.5253.042.021055.0369.5253.042.022055.0313.0253.042.023056.0255.0253.042.024057.0196.5253.042.025057.0138.0253.042.026058.079.0253.042.027058.0253.024false11Arial Bold115193'473.0268.011Arial Bold1151105'-5.0269.01102550255Arial112111Ribosome-106.0141.02true492269255192128255Arial Bold Italic3112123Stop codon
next413.0211.025false31.200000000000017281.3833333333335531.38604875258617282.138832398505770.00643477904868609750.01988800254028840626false31.36780278288308266.61010861963070.0066948142639407670.01901625636414286425false50.400000000000006281.3833333333335550.51425702757615281.809843930486860.0038664309668067440.002786957605130686530false50.0615404736145264.10388595964497-0.007391028363923357-0.01655345529173217825false69.6281.3833333333335569.90243736396278281.5116111731339-0.0052958816522767940.00402548645400261128false69.53151830974336265.3880710078786-0.00832334409559221-0.00821296913272403725false88.79999999999998281.383333333333589.03287961599162281.74308897627792.5761423554505945E-4-0.0027837243311641626false88.95161150024403266.65908871516984-0.00257843467766915660.01313764463538232225false107.99999999999997281.3833333333335108.0965929947008281.46759925375950.0182961590306919930.00154291168205488126false107.72622854522398265.10225345969410.0050170450150769080.0083589319287734525false127.19999999999996281.3833333333335126.78536210644253281.235603052595250.002116112113194255-0.01526892390179804428false126.64792365512724264.24654134387510.009049517339632860.00839068477460256925false146.39999999999995281.3833333333335146.12957811396709281.339769232201660.0059938986431170740.001550160749349214727false145.79361307655967264.157137781964930.002874020313773066-0.00782376600337002625false165.59999999999994281.3833333333335165.1998234097959281.680178867101860.022728303780799635-0.01284329994616580427false165.0433074331611265.0356679047097-0.0071847226540610425-0.00410064599592304225false184.79999999999993281.3833333333335184.22478432190115281.55159672180974-0.003795803651109752-0.01535251283090112426false183.95414298000077265.5282280321339-0.00601646356945518750.001310691626775599425false203.99999999999991281.3833333333335203.3897336550143281.39798490297596-0.0123385800656289140.0180250735721340730false203.76234699574204264.967185159520740.006196246809717935-0.00739351418944927925false223.1999999999999281.3833333333335223.47367203050715281.80082900285050.0058470197323419090.01641631401087711326false223.7306411279818265.1634512541866-0.00126440076682044820.00925823405982988625false242.3999999999999281.3833333333335242.60620745390213281.665630076229040.003142884930991497-0.01408809333073643627false242.3539032167377265.071501485775850.0022216598012669510.003245004255535046425false261.5999999999999281.3833333333335261.2757706848361281.81896940160993-0.005976611479318017-0.01584607000135123527false261.17859022844874265.35780920016657-6.538815012825194E-40.02494813125482308525false280.79999999999995281.3833333333335281.0396566248487281.71405251424494-0.0181785687011135170.002302372174617817630false280.9635650956805264.76585303509984-0.00189327897026112140.003870195289986249725false299.9999999999999281.3833333333335300.56101459990896281.26162678048210.013929951913877270.01558763234251727726false300.6606545933855265.34880698408540.0047502447491132044-0.00499044051120646625false319.19999999999993281.3833333333335319.279360927135281.41386969880180.015175190809796655-0.01176044760178067628false319.8867986001927265.59089385501520.00326973526051300639.203477826408961E-425false338.4281.3833333333335338.70072944436515281.66322972701346-0.004303726006635417-0.01178800675324081928false338.8039755201591265.1477772862917-0.0014759623186075164-0.0089034307448738425false357.5999999999999281.3833333333335358.32302244230436281.14908541390530.00225570133343898146.402189863316969E-428false358.19375108244986264.0699338124907-0.001377780406190863-0.01448727647211128825false376.79999999999995281.3833333333335377.82362754357666280.93609324541420.003784813666358398-0.0169742253869199327false378.1395111776653264.02611814094877-0.0083180768861885330.01022267851687967925false395.9999999999999281.3833333333335396.4354300302287281.389473172973-0.012730477010462305-0.00678689032876081326false397.17419676083716265.8764352673222-0.0222910729281059340.0156622157379329225false415.19999999999993281.3833333333335415.19188046836297281.71303077591847-5.63838662387686E-4-0.01986842672412078227false414.6169358320722266.2905778749411-0.016980598708241347-0.002564117339164700525false434.4281.38333333333344433.5621944420658281.14563895566687-0.011483207707222422-0.01392019328167989930false433.17856520845686264.719724548972350.0135130148371931486.261684443663949E-425false453.5999999999999281.38333333333344452.416145004199281.324935113155-0.02440944141357528-0.0040641181426099628false452.4334725652183264.276384529267260.025602490833526410.02102205645281494625false472.79999999999995281.38333333333344471.3153550141517282.0105917382043-0.0277014703934456880.04731607074726440530false471.5544100246159265.20739884270020.0195016795247465080.01326189046240637912GGC1182.86817768128563106.371176388892850.01323710781780586-0.0332271200819549819CCC1294.86561269778747102.75618944422087-0.055180485395173780.058309326359375911-1.0GAG-2261.0643786023803198.76438405220980.0137675981332241110.0271472319000185545GCT166.22725350568176159.2489127427468-0.006335718335080537-0.0170506414225471875GCC1139.33776963301025101.861550054784770.059694557571082960.082614134328596177AAC-1355.9427310225146172.302055168200780.0021381309412451610.0421660580162262461.0CGG-2199.47712447533976213.71152556461323-0.0242027672542297760.02389354725674739210CAG-1119.42332079115283188.8355214062396-0.013884215258314436-9.330452710544702E-415CTG119.948389922302066200.54760266073643-0.0093944993349531730.01731596231609858-1.0GAC-2162.63124097428127126.761604786218560.034133110178137464-0.00879556542862936512GGC1260.8667159743841474.088727321073620.052130172299630380.0471369540801052921ACC-1388.98297386877584104.739172353047954.964652137818016E-40.002094096758279304523TAC1229.0182.00.0242547399945750380.007492500764242609131.0CAC-2482.63722328041393208.72335339146463-0.063959242479572550.003625861433435156421ACC-1348.06106295939776135.521762841965940.023956851430646083-0.01732229185634034614ATC1161.85707756288843162.439134509231650.0139681497938158850.05096685158507547510CAG-197.59812221071103250.84878902044320.09152672695554114-0.00829302586020350823TAC1159.587112398568193.415314593353470.0077709707197641440.0245241040252744237AAC-1464.13593819810797121.758401263043-0.025353311205352840.00676403113465365422TGG2295.831886905047944.12715646632607-0.017879656081433826-0.0581419922974610117ATG171.0190.0-0.04543700230040869-0.01274035247888199324GTT1294.0223.021ACC-1225.87880443326202125.20921650617146-0.00133813210556712-0.00875244633998841323TAC134.0234.0-0.03118943793296847-0.02608373742958543131.0CAC-2311.1448650099901115.15985505333148-0.014271759690742377-0.004075659154061825518TTC2370.0196.08-1.0GAC-2443.9445264681965687.177337560757020.021557707345001863-0.07402714998859652131.0CAC-2260.0147.020AGC-1314.1550650029145185.95738731098990.083546620787072230.00625231062620969624GTT1116.00646211161487155.4872632198844-0.00941242512217054-0.0328144214816641418TTC2117.73335851413295122.299379440812170.07413095656234829-0.04772846313754918617ATG1178.026.0-6.825140548876185E-44.4259908383003445E-422TGG246.262276719155494169.6417600681849-0.0194391357714086760.092711964963137157AAC-153.510796547605778.59507383274465-0.00241560008616144430.002924111956618963420AGC-141.05410523253761107.727075054944-0.04479649660485023-0.0481877252295634214ATC1222.18822934432745103.98442517243755-0.00232369644248202460.033543297078802368-1.0GAC-2350.86430427085674100.76600633867328-0.0183138966759555270.0228869950928212548-1.0GAC-2479.8408449620772681.29240678198840.016926930901261310.003460818360212637514ATC1487.62549055906953120.40901820711050.009684046112923077-0.0102028005825733161.0CGG-2473.20236356204646166.347519875880440.018182749836844920.04695253247814859521ACC-1460.40280310074036250.436782621805630.020226473350390198-0.0464737861182399817ATG1391.0226.021ACC-1325.0224.020AGC-1252.47640809100753214.56215067534720.015925445841094028-0.055933241797467520AGC-1179.0271976197248217.714661712846550.011354344790740893-0.00308714381281894614ATC1325.5416123571881771.96149588423981-2.3108849110166615E-50.01080125673748626919CCC1330.9591175897221100.97158087331270.012177648079627673-0.0362430811892643610CAG-160.8863556253918938.156261936719470.071648068535330720.02251621305533654815CTG1116.4715978792934462.800179054072196-0.0251407323946668783.847442164499942E-5161.0AAG-2215.2110649394465761.3176103885756-0.0484120239661262050.049051624711390778-1.0GAC-2278.454069745818933.587980285814210.011637752621957514-0.001090317801946612819CCC1391.022.022TGG2450.025.07AAC-1323.9394878832671341.0610934297313150.0207798921896180860.01928904139009779861.0CGG-2303.5080152603606523.313518787748320.020578501782851512-0.0647803184360159222TGG2185.1816423682768457.28583882082655-0.021342720641712908-0.027691632145330266131.0CAC-2250.9569844801598310.6009440908189530.082915437909793720.0446831133284121911-1.0GAG-285.45528017681619.0452598879322820.0290294720999259120.02002557196742993412GGC179.9362207328709158.13167135702780.0616391689777972050.0825936375310756717ATG130.47729834806275719.636723965312772-0.054166320572153065-0.010306060306615998-1.0GAC-238.23743036423254444.183914988249036-0.0415086846548040550.0577844516120504668-1.0GAC-287.49718720489702155.940129691191320.0107035480178556320.04295141431273721ACC-139.519679648490374210.62453186957340.031307708624599960.0531658527635310114ATC1200.3008047582699294.722188604193490.04016022519080540.0405624407475875912GGC1402.053.07AAC-1440.057.09TGC1401.0144.09TGC1211.0153.09TGC1139.027.0131.0CAC-286.0102.0161.0AAG-2412.0119.018TTC2360.057.0161.0AAG-2142.0184.0161.0AAG-2258.0108.04647116.00.22316.80.2219.20.24516.80.24219.20.26716.80.26419.20.28916.80.28619.20.2101116.80.210819.20.2121316.80.2121019.20.2141516.80.2141219.20.2161716.80.2161419.20.2181916.80.2181619.20.2202116.80.2201819.20.2222316.80.2222019.20.2242516.80.2242219.20.2262716.80.2262419.20.2282916.80.2282619.20.2303116.80.2302819.20.2323316.80.2323019.20.2343516.80.2343219.20.2363716.80.2363419.20.2383916.80.2383619.20.2404116.80.2403819.20.2424316.80.2424019.20.2444516.80.2444219.20.2464716.80.2464419.20.2211.570796326794896650.0321.570796326794896650.04321.570796326794896650.05241.570796326794896650.06541.570796326794896650.07461.570796326794896650.08761.570796326794896650.09681.570796326794896650.010981.570796326794896650.0118101.570796326794896650.01211101.570796326794896650.01310121.570796326794896650.01413121.570796326794896650.01512141.570796326794896650.01615141.570796326794896650.01714161.570796326794896650.01817161.570796326794896650.01916181.570796326794896650.02019181.570796326794896650.02118201.570796326794896650.02221201.570796326794896650.02320221.570796326794896650.02423221.570796326794896650.02522241.570796326794896650.02625241.570796326794896650.02724261.570796326794896650.02827261.570796326794896650.02926281.570796326794896650.03029281.570796326794896650.03128301.570796326794896650.03231301.570796326794896650.03330321.570796326794896650.03433321.570796326794896650.03532341.570796326794896650.03635341.570796326794896650.03734361.570796326794896650.03837361.570796326794896650.03936381.570796326794896650.04039381.570796326794896650.04138401.570796326794896650.04241401.570796326794896650.04340421.570796326794896650.04443421.570796326794896650.04542441.570796326794896650.04645441.570796326794896650.04744461.570796326794896650.0