Note: A PERL script written by Charlie Bond and modified locally is used in this example.
sam_at_in prot.pdb
mol prot
obj prot
z ; end
centre_atom 121 cd1
Draw the map (Note: color does not matter here, you will define it later in MolScript)
map_file 2fofc.omap
map_obj mapobj
map_par 12 12 12 1. lime_green 0.5 0.1 1
map_ac
map_dr
Output the map drawing commands:
Plot_setup eden.plt [return, return, return]
Plot
Now outside of O, in a UNIX (X-term) window give the following commands:
setup ono (if not done already)
plt2mol MAPOBJ_MAP 0.27 0.51 0.71 < eden.plt > eden.obj
Where the argument "MAPOBJ_MAP" is the object you want from the eden.plt file, and the three real numbers (0.27 0.51 0.71) are the rgb numbers for the color you want.
In the X-term window, edit a file called mol.in containing the following:
plot
background rgb 1.0 1.0 1.0 ;
window 15.0 ;
slab 5.5 ;
read m1 prot.pdb;
transform atom * by centre 11.035 43.882 24.733
;
ball-and-stick sphere 0.0 0.0 0.0 10.0 ;
set objecttransform on ;
object eden.obj;
end_plot
Where the window and slab values are first guesses, prot.pdb is your protein PDB file, the coordinates after centre are the coordinates of the atom you centered on in O to draw the map, and eden.obj is the external object (the map) that you are reading into MolScript.
Then type:
setup molscript
molscript -gl -in mol.in
On the MolScript OpenGL graphics window use the Left Mouse Button to orient your image as you want it, then from the Right Mouse Button, click Output view.
Something like the following will appear on the X-term window:
by rotation
-0.58208 0.281331 -0.762913
0.649295 0.725614 -0.227816
0.489489 -0.627962 -0.605032
Copy and paste these lines into your mol.in file so that it looks like this:
plot
background rgb 1.0 1.0 1.0 ;
window 15.0 ;
slab 5.5 ;
read m1 prot.pdb;
transform atom * by centre 11.035 43.882 24.733
by rotation
-0.58208 0.281331 -0.762913
0.649295 0.725614 -0.227816
0.489489 -0.627962 -0.605032
;
ball-and-stick sphere 0.0 0.0 0.0 10.0 ;
set objecttransform on ;
object eden.obj;
end_plot
Now, by trial and error set the window, slab, atomcolour, etc. in the mol.in file using MolScript commands and clicking "Re-read input file" in the MolScript OpenGL graphics window after each editing change:
plot
background rgb 1.0 1.0 1.0 ;
window 12.0 ;
slab 3.9 ;
read m1 prot.pdb;
transform atom * by centre 11.035 43.882 24.733
by rotation
-0.58208 0.281331 -0.762913
0.649295 0.725614 -0.227816
0.489489 -0.627962 -0.605032
;
set atomradius atom * 0.8 ;
set atomcolour atom * red ;
set colourparts on ;
ball-and-stick sphere 0.0 0.0 0.0 10.0 ;
set objecttransform on ;
object eden.obj;
end_plot
Once you have it the way you want it, type:
molscript -ps < mol.in > mol.ps
Last Modified: Monday, 05-Oct-1998 10:01:43 EDT