CPK Model

MSDRAW renders various atomic representations for a protein molecule. An example of a CPK 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 cpk.ms containing the following:

   molecule protein pdb4pti.cln
   protein color = grey # default, mainly carbons
   protein ball = 1.8
   oxygens = atom matches O
   oxygens color = red
   oxygens ball = 1.6
   nitrogens = atom matches N
   nitrogens color = blue
   nitrogens ball = 1.7
   sulfurs = atom matches S
   sulfurs color = yellow
   sulfurs ball = 2.0
   ball_and_stick # no sticks since no connect
   atom_coloring # use colors specified above

4.Type the following command:

    msdraw -i cpk.ms -r cpk.rgb

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

    ipaste cpk.rgb

Last CSB Revision: Friday, 07-Feb-1997 16:42:39 EST