2.2250.0false400250400.01.3576filenamepage10$1.mmldate1220909395583urlC:\Documents and Settings\qxie\Desktop\pna\page10$1.mmlsize70262codebaseC:\Documents and Settings\qxie\Desktop\pnado my job200My taskshow selectionhalo off;
select atom within (%atom[66].rx, "%height-8", %width, "%atom[74].rx-%atom[66].rx");
set kelvin 3000;
select atom not selected;
set kelvin 6000;
select atom none;
if(%model_time<5000);
set %at1 -1;
set %at2 -1;
set %n 67;
set %type complementaryType(%atom[%n].id, RNA);
set %sp -1;
set image[0].x %image[0].x+2;
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>67); // move the text box to invisible
set textbox[2].x %textbox[2].x-1;
endif;
if(%n>75); // 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 10;
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);
else;
//what to do?
endif;
endif;
show selectionhalo on;
255255192255Nonepolymerase.gif21-129.016.024false11Arial Bold11566class org.concord.mw2d.models.Atom113' 111.19722747802734220.2567291259765611Arial Bold11574class org.concord.mw2d.models.Atom12 5'187.99224853515625219.382202148437511202550255132RNA 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