// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
var s_co4bases =
"define tmp selected\n\
\
select all\n\
labels off\n\
select backbone\n\
color [180,90,0]\n\
select A and not backbone\n\
color [96,96,255]\n\
select T and not backbone\n\
color yellow\n\
select G and not backbone\n\
color green\n\
select C and not backbone\n\
color [255,32,32]\n\
\
select tmp\n\
";

// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
var s_at2 =
"reset\n\
select all\n\
spacefill off\n\
wireframe 0\n\
rotate z 90\n\
rotate y 10\n\
zoom 200\n\
\
delay 0.5\n\
\
#TRIM OFF ENDS UNTIL JUST 2 BASE PAIRS LEFT\n\
hbonds off\n\
restrict 2-18:d or 21-37:e\n\
delay 0.1\n\
restrict 3-17:d or 22-36:e\n\
delay 0.1\n\
restrict 4-16:d or 23-35:e\n\
delay 0.1\n\
restrict 5-15:d or 24-34:e\n\
delay 0.1\n\
restrict 6-14:d or 25-33:e\n\
delay 0.1\n\
restrict 7-13:d or 26-32:e\n\
delay 0.1\n\
restrict 8-12:d or 27-31:e\n\
delay 0.1\n\
restrict 9-11:d or 28-30:e\n\
delay 0.1\n\
restrict 10:d or 29:e\n\
delay 0.1\n\
\
define current selected\n\
center selected\n\
move 0 90 0 200 0 0 0 0 2 30\n\
color hbonds white\n\
hbonds\n\
";

// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
var s_gc2 =
"reset\n\
select all\n\
spacefill off\n\
wireframe 0\n\
rotate z 90\n\
rotate y 10\n\
zoom 200\n\
\
delay 0.5\n\
\
#TRIM OFF ENDS UNTIL JUST 2 BASE PAIRS LEFT\n\
hbonds off\n\
restrict 2-18:d or 21-37:e\n\
refresh\n\
delay 0.1\n\
restrict 3-17:d or 22-36:e\n\
refresh\n\
delay 0.1\n\
restrict 4-16:d or 23-35:e\n\
refresh\n\
delay 0.1\n\
restrict 5-15:d or 24-34:e\n\
refresh\n\
delay 0.1\n\
restrict 6-14:d or 25-33:e\n\
refresh\n\
delay 0.1\n\
restrict 7-13:d or 26-32:e\n\
refresh\n\
delay 0.1\n\
restrict 8-12:d or 27-31:e\n\
refresh\n\
delay 0.1\n\
restrict 9-11:d or 28-30:e\n\
refresh\n\
delay 0.1\n\
restrict 9-10:d or 29-30:e\n\
refresh\n\
delay 0.1\n\
restrict 9:d or 30:e\n\
refresh\n\
delay 0.1\n\
\
define current selected\n\
center selected\n\
move 0 90 30 200 0 0 0 0 2 30\n\
color hbonds white\n\
hbonds\n\
";

// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

var s_bases =
"select current; spacefill off; wireframe 0; hbonds; " +
"select current and not (backbone or hydrogen); wireframe 0.3;";

var s_backbone =
"select current; spacefill off; wireframe 0; hbonds; " +
"select current and backbone and not hydrogen; wireframe 0.3;";

var s_hbonds =
"spacefill off; wireframe 0; hbonds 0.3;";

var s_thin =
"spacefill off; wireframe 0; hbonds;";

var s_thick =
"spacefill off; wireframe 0.3; hbonds 0.3";

var s_spacefill =
"wireframe off; hbonds 0.3; spacefill;";


// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

var s_replicate =
"wireframe 0\n\
delay 0.6\n\
\
select :d\n\
color [128,128,128]\n\
delay 1\n\
\
restrict not :d\n\
delay 1\n\
\
select backbone\n\
color [180,90,0]\n\
select A and not backbone\n\
color [96,96,255]\n\
select T and not backbone\n\
color yellow\n\
select G and not backbone\n\
color green\n\
select C and not backbone\n\
color [255,32,32]\n\
\
select 1-2:d\n\
wireframe 0.3\n\
refresh\n\
rotate y 1\n\
delay 0.4\n\
rotate y 1\n\
\
select 1-3:d\n\
wireframe 0.3\n\
refresh\n\
delay 0.4\n\
rotate y 1\n\
\
select 1-4:d\n\
wireframe 0.3\n\
refresh\n\
delay 0.4\n\
rotate y 1\n\
\
select 5:d\n\
wireframe 0.3\n\
refresh\n\
delay 0.4\n\
rotate y 1\n\
\
select 1-6:d\n\
wireframe 0.3\n\
refresh\n\
delay 0.4\n\
rotate y 1\n\
\
select 1-7:d\n\
wireframe 0.3\n\
refresh\n\
delay 0.4\n\
rotate y 1\n\
\
select 1-8:d\n\
wireframe 0.3\n\
refresh\n\
delay 0.4\n\
rotate y 1\n\
\
select 1-9:d\n\
wireframe 0.3\n\
refresh\n\
delay 0.4\n\
rotate y 1\n\
\
select 1-10:d\n\
wireframe 0.3\n\
refresh\n\
delay 0.4\n\
rotate y 1\n\
\
select 1-11:d\n\
wireframe 0.3\n\
refresh\n\
delay 0.4\n\
rotate y 1\n\
\
select 1-12:d\n\
wireframe 0.3\n\
refresh\n\
delay 0.4\n\
rotate y 1\n\
\
select 1-13:d\n\
wireframe 0.3\n\
refresh\n\
delay 0.4\n\
rotate y 1\n\
\
select 1-14:d\n\
wireframe 0.3\n\
refresh\n\
delay 0.4\n\
rotate y 1\n\
\
select 1-15:d\n\
wireframe 0.3\n\
refresh\n\
delay 0.4\n\
rotate y 1\n\
\
select 1-16:d\n\
wireframe 0.3\n\
refresh\n\
delay 0.4\n\
rotate y 1\n\
\
select 1-17:d\n\
wireframe 0.3\n\
refresh\n\
delay 0.4\n\
rotate y 1\n\
\
select 1-19:d\n\
wireframe 0.3\n\
refresh\n\
delay 0.4\n\
\
move 0 5 0 0    0 0 0 0  1\n\
move 0 -22 0 0    0 0 0 0  2\n\
\
select all\n\
";


// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
var s_codons =
"select all\n\
hbonds off\n\
set fontsize 12\n\
wireframe 0\n\
restrict not (2,3,36,37)\n\
translate x -5\n\
\
delay 0.6\n\
\
select :d\n\
color [128,128,128]\n\
delay 1\n\
move 45 0 0  0  0 0 0  0  2 30\n\
delay 1.\n\
\
color white\n\
restrict not :d\n\
delay 1\n\
move 45 0 0  0  0 0 0  0  2 30\n\
delay 1.\n\
\
select 21-23 and not backbone\n\
wireframe 0.3\n\
delay 0.2\n\
wireframe 0\n\
delay 0.2\n\
wireframe 0.3\n\
delay 0.2\n\
wireframe 0\n\
delay 0.2\n\
wireframe 0.3\n\
delay 0.2\n\
\
select atomno=465\n\
label G\n\
select atomno=440\n\
label G\n\
select atomno=421\n\
label C\n\
\
delay 1\n\
\
select 24-26 and not backbone\n\
wireframe 0.3\n\
delay 0.2\n\
wireframe 0\n\
delay 0.2\n\
wireframe 0.3\n\
delay 0.2\n\
wireframe 0\n\
delay 0.2\n\
wireframe 0.3\n\
delay 0.2\n\
wireframe 0\n\
\
select atomno=527\n\
label G\n\
select atomno=505\n\
label G\n\
select atomno=484\n\
label A\n\
\
delay 1\n\
\
select (27-29) and not backbone\n\
wireframe 0.3\n\
delay 0.2\n\
wireframe 0\n\
delay 0.2\n\
wireframe 0.3\n\
delay 0.2\n\
wireframe 0\n\
delay 0.2\n\
wireframe 0.3\n\
delay 0.2\n\
\
select atomno=589\n\
label T\n\
select atomno=570\n\
label C\n\
select atomno=549\n\
label A\n\
\
delay 1\n\
\
select (30-32) and not backbone\n\
wireframe 0.3\n\
delay 0.2\n\
wireframe 0\n\
delay 0.2\n\
wireframe 0.3\n\
delay 0.2\n\
wireframe 0\n\
delay 0.2\n\
wireframe 0.3\n\
delay 0.2\n\
wireframe 0\n\
\
select atomno=648\n\
label C\n\
select atomno=631\n\
label T\n\
select atomno=609\n\
label G\n\
\
delay 1\n\
\
select (33-35) and not backbone\n\
wireframe 0.3\n\
delay 0.2\n\
wireframe 0\n\
delay 0.2\n\
wireframe 0.3\n\
delay 0.2\n\
wireframe 0\n\
delay 0.2\n\
wireframe 0.3\n\
delay 0.2\n\
\
select atomno=709\n\
label C\n\
select atomno=689\n\
label T\n\
select atomno=670\n\
label C\n\
\
delay 1.\n\
move 45 0 0  0  0 0 0  0  2 30\n\
delay 1.\n\
\
select atomno=75\n\
label 'mRNA:gag'\n\
\
delay 0.4\n\
\
select atomno=143\n\
label 'mRNA:gac'\n\
\
delay 0.3\n\
\
select atomno=203\n\
label 'mRNA:agu'\n\
\
delay 0.3\n\
\
select atomno=261\n\
label 'mRNA:ccu'\n\
\
delay 0.3\n\
\
select atomno=317\n\
label 'mRNA:ccg'\n\
\
delay 1.\n\
move 45 0 0  0  0 0 0  0  2 30\n\
delay 1.\n\
\
select atomno=75\n\
label 'mRNA:gag=Glu'\n\
\
delay 0.3\n\
\
select atomno=143\n\
label 'mRNA:gac=Asp'\n\
\
delay 0.3\n\
\
select atomno=203\n\
label 'mRNA:agu=Ser'\n\
\
delay 0.3\n\
\
select atomno=261\n\
label 'mRNA:ccu=Pro'\n\
\
delay 0.3\n\
\
select atomno=317\n\
label 'mRNA:ccg=Pro'\n\
\
move 45 0 0  0  0 0 0  0  2 30\n\
select :e and not (2,3,36,37,atomno=753)\n\
define current selected\n\
";

// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
var s_reset =
"select all\n\
labels off\n\
define current selected\n\
spacefill off\n\
wireframe 0\n\
hbonds off # to hide thick hbonds\n\
hbonds # to make them all dotted\n\
color hbonds white\n\
reset\n\
rotate z 90\n\
rotate y 10\n\
zoom 200\n\
";

// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -