!------------------------------------------------------!
!                  This is Bobscript                   !
!------------------------------------------------------!
! Example  8: Transparent surface         by L. Esser  !
!------------------------------------------------------!

macro nucleotide

  set atomcolour atom C*  hsb 0.087 1.0 0.8;
  set atomcolour atom CA1 hsb 0.0 0.0 0.95;
  set sticksegments 2;
  colour ball-and-stick by atom ;

  set colourdepthcue       0.0;  ! Make sure calcium is really white !
  set atomradius atom CA1  2.6;  ! 4x larger than Angstroem
  ball-and-stick in type   CAL;
  set colourdepthcue       0.3;  ! Now we can reset the colourdepthcue.

  set bonddistance 1.7;
  ball-and-stick in residue 800 ;

  set bonddistance 2.3;
  ball-and-stick require in type APS and either atom S* or atom P*;

end_macro

macro residues

  set depthcue 0.5;
  set colourdepthcue 0.5;

  colour second-ramp from hsb 0.166  0.31 0.9  
                     to   hsb 0.166  0.31 0.9 by sequence from 112 to 417;

  colour trace ramp second-ramp;

  set linewidth     2.0; !- width of the trace
  set sticksegments   2; !- nothing complex
  trace from 112 to 417;
  
  set atomcolour atom C* hsb 0.166  0.31 0.9;
  colour ball-and-stick by atom;
  set sticksegments 2;

  ball-and-stick require in either type ARG, type LYS, type HIS,
                                   type GLU or type ASP
                                   and not either atom C, atom N or atom O;
  
end_macro

plot
  window 72.0;
  slab   55.0;
  set colourdepthcue  0.3; 
  set linewidth       1.0;
  set shading         1.0;
  set shadingexponent 2.0;
  set smoothsteps       3;
  set splinefactor    1.0;
  set strandthickness 0.5;
  set strandwidth     1.8;
  set segments        25;

  read no-h mol "example.pdb" ; ! Read pdb file

  transform atom * by centre position atom * ; 
  transform atom * by rotation @new_view.in;

  !------------------------------!
  !     Draw a Calpha trace      !
  !------------------------------!

  $residues

  !------------------------------!
  !       Draw nucleotide        !
  !------------------------------!
 
  !$nucleotide

end_plot