!------------------------------------------------------!
!                  This is Bobscript                   !
!------------------------------------------------------!
! Example  8: Surfaces 2                  by L. Esser  !
!------------------------------------------------------!

macro nucleotide

  set atomcolour atom C*  hsb 0.0 0.0 0.6;
  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 ca-trace

  colour second-ramp from hsb 0.0       0.85 0.9 via 
                          hsb 0.1666    0.85 0.9 via
                          hsb 0.3333    0.85 0.9 via
                          hsb 0.6666    0.85 0.9   
                     to hsb 0.8666 0.85 0.9 by sequence from 250 to 313;

  colour trace ramp second-ramp;

  set linewidth  6.0;
  set sticksegments 10;
  trace from 250 to 313 ;
  
end_macro

macro residues

  set sticksegments 2;
  set atomcolour atom C* hsb 0.0 0.0 0.6;
  set atomcolour atom N* hsb 0.6667 0.8 1.0;

  colour ball-and-stick by atom; 
  ball-and-stick require in from 250 to 313 and not 
                  either atom C, atom N or atom O;


end_macro

plot
  window 50.0;
  slab   50.0;
  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" ;

  !-------------------------------------------------------------------! 
  ! Now the next two lines are extremely important when you want 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 residues          !
  !------------------------------!

  $residues

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

end_plot