!------------------------------------------------------!
!                  This is Bobscript                   !
!------------------------------------------------------!
! Example  6: Special characters          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 side-chains
     
  set sticksegments     2;
  set bonddistance      2.0;
  set atomradius atom * 0.6;

  colour ball-and-stick by atom;

  ball-and-stick require 

                    not atom N, 
                    not atom O, 
                    not atom C, 
                    not atom H* 

                  and in either 

                    residue 386, 
                    residue 388
                 or 
                    residue 373 ;

end_macro


macro make-bonds

  set colourdepthcue  0.0;
  set bonddistance    3.0;
  set linewidth       1.8; ! Line thickness will be used as the radius of the 
                           ! sphere in 'fragment'

  set linecolour rgb  1.0 1.0 1.0 ; ! c1 refers to white; c2 to black 

  set bonddistance    3.1; ! we have rather long bonds here. Ca-O about 2.6 A

  bonds in type CAL atom O* ;

end_macro

plot
  window 10.0;
  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        25;

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

  transform all by centre position atom CA1
                by rotation @new_view.in 
                by translation 0.0 0.0 0.0 ;

  !-------------------------------------------!
  ! Make strands go through the CA positions. ! 
  !-------------------------------------------!

  set fixedcalphas either residue 386, residue 373 or residue 388;

  !------------------------------! !----------------------------------------!
  ! Draw now secondary structure ! ! Two strands are enough in this example !
  !------------------------------! ! So we don't use "2nd.inb"              !
                                   !----------------------------------------!
  set tworamps on;
  colour second-ramp  hsb 0.333 0.95 0.20 ;
  colour strand hsb       0.300 0.95 0.70 ;

         strand from 369 to 375 ;
         strand from 381 to 389 ;


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

  !------------------------------!
  !    Draw some residues        !
  !------------------------------!
 
  $side-chains

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

  $make-bonds

end_plot