Ball and Stick Model

MSDRAW renders various atomic representations for a protein molecule. An example of a ball and stick model is shown below:

These results were obtained for 4pti by the following commands:

1. Get the PDB file

    getentry 4pti

2. Extract the ATOM records:

    extract pdb4pti.ent 
(which creates a file called pdb4pti.cln containing only ATOM records)

3. Create a file called containing the following:

   light_source -0.5 1.0 1.0
   shading_model 0.2 0.2 0.4 0.2 2.0
   molecule protein pdb4pti.cln
   tolerance 0.25
   elbow 0.5
   connect protein # creates sticks
   protein color = grey
   oxygens = atom matches O
   oxygens color = red
   nitrogens = atom matches N
   nitrogens color = blue
   sulfurs = atom matches S
   sulfurs color = yellow
   ball_radius 0.3
   bond_radius 0.1
   atom_coloring # use colors specified above

4.Type the following command:

    msdraw -i -r bas.rgb 

5. View the cpk.rgb image with the following command:

    ipaste bas.rgb

Last CSB Revision: Friday, 07-Feb-1997 16:42:25 EST