!------------------------------------------------------!
!                  This is Bobscript                   !
!------------------------------------------------------!
! Example  7: Surfaces 1                  by L. Esser  !
!------------------------------------------------------!

macro nucleotide
 
  set stickradius  0.3;
  set atomradius atom * 2.0;
  set atomradius either atom S* or atom P* 3.0;
  set atomcolour atom C*  hsb 0.0 0.0 0.3;
  set atomcolour atom CA1 hsb 0.0 0.0 1.0;
  set sticksegments 2;
  colour ball-and-stick by atom ;

  set colourdepthcue       0.0;  ! Make sure calcium is really white !
  set atomradius atom CA1  4.0;  ! 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 ca-trace

  set linecolour hsb 0.0 0.0 0.5;  ! 50% gray
  set linewidth  2.0;
  trace amino-acids ;
  
end_macro


plot
  window 55.0;
  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        5;

  read no-h mol "example.pdb" ;

  !-------------------------------------------------------------------! 
  ! Now the next two lines are extremely important when you want to   !
  ! to use the matrix and translation vector printed in the log file. !
  !-------------------------------------------------------------------! 

  transform atom * by centre position in residue 800 ; 
  transform atom * by rotation @new_view.in;

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

  $ca-trace

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

end_plot