MOLSCRIPT Ball and Stick Stereo Example

The input file below assumes you have the coordinates for your model in a file called rns.cln in the same directory. In this case only residues 1 to 15 will be drawn.

macro delete_hydrogens          ! assumes: 1) old molecule is called tmp
  copy mol not atom H*;         !          2) no molecule mol is defined
  delete tmp;
end_macro

macro black_white_atoms		!can be called later for grayscale
  set atomcolour atom C* black,
      atomcolour atom N* grey 0.2,
      atomcolour atom O* grey 0.5,
      atomcolour atom P* grey 0.8,
      atomcolour atom S* grey 0.8;
end_macro

macro colored_atoms		!can be called later for color
  set atomcolour atom C* grey 0.5,
      atomcolour atom N* blue,
      atomcolour atom O* red, 
      atomcolour atom S* yellow, 
      atomcolour atom P* green ;
end_macro

macro trans			!can be called later to rotate sideways
    transform atom *
    by centre position atom *           !center of plot = center of mass
    by rotation z 90.0
!    by rotation x 20.0
!    by rotation y 0.0
    ;
end_macro

plot noframe	!left side (on bottom of page as you see it)

!The next line creates a plot which will overlap with the right side
!to bring the two images closer together if stereo separation is too much.
!i.e., 410 instead of 390 for the yupperright of the left (lower as you
!see it) image.

! xlowerleft.r ylowerleft.r xupperright.r yupperright.r
!  area 50.0 40.0 550.0 390.0;
  area 50.0 40.0 550.0 410.0;
  
  window 25.0;			!sizes the window and thus the margins

  read tmp "2rns.cln";		!a pdb file

  $delete_hydrogens		!macro to delete hydrogens

  $trans			!call the rotation macro

  transform atom * 
    by centre position atom *		!center of plot = center of mass
    by translation 4.0 2.0 0.0		!4x to center and 2y to move it
					!up a little to close the stereo
					!separation
    by rotation x -3.0			!left stereo rotation
    ;

  $black_white_atoms		!choose color

  ball-and-stick require in amino-acids	!not water, detergent, salts,etc.
    and in from 1 to 15 ;		!defines S peptide

  set labelsize 20.0, labelrotation on;	!what labels to be rotated 90 deg

  label 4.0 7.0 0.0 "PHE";	!4x, 7y, 0z to position next to ring

end_plot

plot noframe	!right side (upper image as you see it on the page)

!  area 275.0 100.0 550.0 700.0;
  area 50.0 390.0 550.0 760.0;

  window 25.0;

  read tmp "2rns.cln";

  $delete_hydrogens 

  $trans

  transform atom *
    by centre position atom *
    by translation 4.0 0.0 0.0
    by rotation x 3.0
    ;

  $black_white_atoms

  ball-and-stick require in amino-acids
    and in from 1 to 15 ;

  set labelsize 20.0, labelrotation on;

  label 4.0 5.0 0.0 "PHE";

end_plot