!------------------------------------------------------!
!                  This is Bobscript                   !
!------------------------------------------------------!
! Example  10: Transparent CPK model      by L. Esser  !
!------------------------------------------------------!

macro nucleotide

  set atomcolour atom C*  hsb 0.667 0.2 0.5;
  set atomcolour atom CA1 hsb 0.0 0.0 0.95;
  set sticksegments 2;
  colour ball-and-stick by atom ;

  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 model-cpk

  ! The standard colour are quite a bit to intense therefore :
  set atomcolour atom C* hsb 0.0 0.0 0.9;
  set atomcolour atom O* hsb 0.0 0.1 1.0;
  set atomcolour atom N* hsb 0.6667 0.1 1.0;
  set atomcolour atom S* hsb 0.1667 0.1 1.0;
  set atomcolour atom P* hsb 0.8333 0.1 1.0;

  ! But at first I want all atoms to have the same "color".
  ! They are all transparent

  set atomcolour atom * hsb 0.0 0.0 0.8;

  set material phong 45.0 specular 0.8 clarity 0.9 options 1 0 0 0 ;
  cpk in type APS ;

end_macro


plot
  window 20.0;
  slab   15.0;
  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        10;

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

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

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

  !------------------------------!
  !  Draw transparent CPK model  !
  !------------------------------!

  $model-cpk

end_plot