!------------------------------------------------------!
!                  This is Bobscript                   !
!------------------------------------------------------!
! Example  4: Density                     by L. Esser  !
!------------------------------------------------------!

macro nucleotide

  set atomcolour atom C*  hsb 0.0 0.0 0.5;
  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 sticksegments     2;
  set bonddistance      2.0;
  set atomradius atom * 0.6;

  colour ball-and-stick by atom;

  ball-and-stick in either from 369 to 374 or from 384 to 389 ;  

end_macro

macro make-bonds

  set colourdepthcue  0.0;
  set bonddistance    3.0;
  set linewidth       2.5;
  set linecolour rgb  1.0 1.0 1.0 ;
  set bonddistance    3.1;

  bonds in type CAL atom O* ;

end_macro

macro e-density

  set maplinewidth 0.8;
  set mapcolour    hsb 0.667 0.7 1.0;
  set map2colour   hsb 0.667 0.7 0.5;

  set coverradius 2.3; 
  
  set material  phong 0 specular 0 clarity 0 ; 
  set colourdepthcue  0.7;

  contour in-out dens at 1.0 covering in either 
                      residue 800,
                      residue 1,
                      from 369 to 374 or
                      from 384 to 389; 
end_macro

plot
  window 22.0;
  slab   16.0;
  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        20;

  !-----------------------!
  !     Read pdb file     !
  !-----------------------!                          

  read no-h mol "example.pdb" ;

  !-----------------------!
  ! Read map file o-style !
  !-----------------------!                          

  map dens "example_2fofc.map" format dsn6  
            around in either residue 800 or residue 276 plus 16;  

  transform all by centre position in residue 800
                by rotation @new_view.in 
                by translation 0.0 6.0 0.0 ;


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

  !--------------------------------------------------!
  ! Draw some residues around the metal binding site !
  !--------------------------------------------------!
 
  $residues

  !------------------------------!
  ! Draw ligand to metal bonds   !
  !------------------------------!

  $make-bonds

  !------------------------------!
  !     Draw electron density    !
  !------------------------------!

  $e-density

end_plot