plot
background grey 1.0;
window 130;
slab 150;
  read mol "align/out2.pdb";


  transform in require molecule mol and residue * 
by translation  0  -30 0
;

  set segments 12;
!    SEMA3A
!First Repeat-RED
set planecolour rgb  1 0 0;
set plane2colour rgb  1 0 0;
  coil from B26 to B30;
  strand from B30 to B34;
  turn from B34 to B35;
coil from B35 to B36;
  helix from B36 to B42;
coil from B42 to B43;
  turn from B43 to B44;
  strand from B44 to B48;
  coil from B48 to B51;
  helix from B51 to B54;
  coil from B54 to B59;
  strand from B59 to B63;
  coil from B63 to B67;
  strand from B67 to B73;
coil from B73 to B75;
strand from B75 to B81;
  coil from B81 to B87;


!Second Repeat-ORANGE
set planecolour rgb  1 0.647 0;
set plane2colour rgb  1 0.647 0;
  strand from B87 to B93;
  coil from B93 to B96;
  helix from B96 to B106;
  coil from B106 to B109;
helix from B109 to B114;
coil from B114 to B117;
  strand from B117 to B124;
  coil from B124 to B127;
  strand from B127 to B134;
  coil from B134 to B139;
  strand from B139 to B146;
  coil from B146 to B154;
  strand from B154 to B158;
  coil from B158 to B162;


!Third Repeat-YELLOW
set planecolour rgb  1 1 0;
set plane2colour rgb  1 1 0;
  strand from B162 to B165;
  coil from B165 to B177;
  strand from B177 to B182;
  coil from B182 to B184;
  strand from B184 to B192;
  coil from B192 to B198;
  strand from B198 to B205;
  coil from B205 to B210;

!Fourth Repeat-GREEN
set planecolour rgb  0 1 0;
set plane2colour rgb  0 1 0;
  strand from B210 to B212;
  coil from B212 to B224;
  strand from B224 to B233;
  coil from B233 to B237;
  helix from B237 to B239;
  coil from B239 to B241;
  strand from B241 to B250;
  coil from B250 to B260;
  strand from B260 to B270;
  coil from B270 to B287;

!Fifth Repeat-CYAN
set planecolour rgb  0 1 1;
set plane2colour rgb  0 1 1;
  strand from B287 to B293;
  coil from B293 to B303;
  strand from B303 to B314;
  coil from B314 to B322;
  strand from B322 to B330;
  coil from B330 to B336;
  strand from B336 to B343;
  coil from B343 to B346;
  helix from B346 to B354;
  turn from B354 to B355;
  strand from B355 to B359;
  coil from B359 to B366;
  strand from B366 to B369;
  coil from B369 to B392;
  helix from B392 to B395;
  coil from B395 to B397;
  helix from B397 to B404;
  coil from B404 to B422;
  

!Sixth Repeat-BLUE
set planecolour rgb  0 0 1;
set plane2colour rgb  0 0 1;
  strand from B422 to B426;
  coil from B426 to B430;
  strand from B430 to B440;
  coil from B440 to B444;
  strand from B444 to B453;
coil from B453 to B457;
strand from B457 to B462;
  coil from B462 to B474;


!Seventh Repeat-PURPLE
set planecolour rgb  0.6275 0.1255 0.9412;
set plane2colour rgb  0.6275 0.1255 0.9412;
  strand from B474 to B481;
  coil from B481 to B490;
  strand from B490 to B495;
  coil from B495 to B499;
  strand from B499 to B505;
  coil from B505 to B508;
  strand from B508 to B513;
  coil from B513 to B520;

set atomcolour atom N* grey 0.2,
         atomcolour atom O* grey 0.2,
         atomcolour atom S* grey 0.2,
         atomcolour atom P* grey 0.2,
         atomcolour atom C* grey 0.2,
         atomradius atom * .75,
         colourparts on;

set bonddistance 2.6 ;

ball-and-stick
either require in residue B103 and either atom CA, atom CB or atom SG
or require in residue B114 and either atom CA, atom CB or atom SG;

ball-and-stick
either require in residue B132 and either atom CA, atom CB or atom SG
or require in residue B141 and either atom CA, atom CB or atom SG;

ball-and-stick
either require in residue B269 and either atom CA, atom CB or atom SG
or require in residue B381 and either atom CA, atom CB or atom SG;

ball-and-stick
either require in residue B293 and either atom CA, atom CB or atom SG
or require in residue B341 and either atom CA, atom CB or atom SG;


cpk in residue B600;
cpk in residue B601;
set colourparts off;


!LABELS


  set labelsize 15.0 ;
  set depthcue 0.0;
  set linecolour black;
  set labeloffset  0.0 0.0 0.0 ;
  label position require atom N and in residue  B26 "N" ;
  set labeloffset  0.0 0.0 0.0 ;
  label position require atom C and in residue B520 "C" ;
  
  read mol2 "align/out.pdb";


  transform in require molecule mol2 and residue * 
by rotation z 85
by translation  0  30 0;


  set segments 2;

!First Repeat-RED
set planecolour rgb  1 0 0;
set plane2colour rgb  1 0 0;
  strand from A45 to A52;
  coil from A52 to A56;
  strand from A56 to A58;
  coil from A58 to A60;
  strand from A60 to A64;
  coil from A64 to A69;
  strand from A69 to A82;
  turn from A82 to A83;
  helix from A83 to A86;
  coil from A86 to A89;

!Second Repeat-ORANGE
set planecolour rgb  1 0.647 0;
set plane2colour rgb  1 0.647 0;
  strand from A89 to A95;
  coil from A95 to A102;
  strand from A102 to A105;
  turn from A105 to A106;
  helix from A106 to A109;
  turn from A109 to A110;
  strand from A110 to A115;
  coil from A115 to A120;
  strand from A120 to A126;
  coil from A126 to A136;

!Third Repeat-YELLOW
set planecolour rgb  1 1 0;
set plane2colour rgb  1 1 0;
  strand from A136 to A140;
  coil from A140 to A143;
  strand from A143 to A152;
  coil from A152 to A156;
  strand from A156 to A163;
  coil from A163 to A165;
  strand from A165 to A169;
  turn from A169 to A170;
  helix from A170 to A173;
  coil from A173 to A176;


!Fourth Repeat-GREEN
set planecolour rgb  0 1 0;
set plane2colour rgb  0 1 0;
  strand from A176 to A181;
  coil from A181 to A185;
  strand from A185 to A193;
  coil from A193 to A197;
  strand from A197 to A205;
  coil from A205 to A207;
  strand from A207 to A213;
  coil from A213 to A216;

!Fifth Repeat-CYAN
set planecolour rgb  0 1 1;
set plane2colour rgb  0 1 1;
  strand from A216 to A223;
  coil from A223 to A229;
  strand from A229 to A234;
  turn from A234 to A235;
  helix from A235 to A238;
  coil from A238 to A241;
  strand from A241 to A245;
  coil from A245 to A249;
  strand from A249 to A253;
  turn from A253 to A254;
  helix from A254 to A258;
  coil from A258 to A260;

!Sixth Repeat-BLUE
set planecolour rgb  0 0 1;
set plane2colour rgb  0 0 1;
  strand from A260 to A265;
  turn from A265 to A266;
  helix from A266 to A269;
  coil from A269 to A273;
  strand from A273 to A279;
  coil from A279 to A284;
  strand from A284 to A289;
  coil from A289 to A293;
  strand from A293 to A297;
  turn from A297 to A298;
  helix from A298 to A301;
  coil from A301 to A305;

!Seventh Repeat-PURPLE
set planecolour rgb  0.6275 0.1255 0.9412;
set plane2colour rgb  0.6275 0.1255 0.9412;
  strand from A305 to A309;
  coil from A309 to A312;
  strand from A312 to A320;
  turn from A320 to A321;
  helix from A321 to A324;
  coil from A324 to A326;
  strand from A326 to A333;
  coil from A333 to A335;
  strand from A335 to A340;

!LABELS


  set labelsize 15.0 ;
  set depthcue 0.0;
  set linecolour black;
  set labeloffset  3.0 0.0 0.0 ;
  label position require atom N and in residue  A45 "N" ;
  set labeloffset  0.0 2.0 0.0 ;
  label position require atom C and in residue A335 "C" ;
  

end_plot