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
3. Create a file called bas.ms 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 ball_and_stick atom_coloring # use colors specified above
4.Type the following command:
msdraw -i bas.ms -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