MSDRAW renders various atomic representations for a protein molecule. An example of a ball and stick with a translucent surface 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. Make the binary surface file prot.pqms for use below:
msroll -m pdb4pti.cln -p 1.4 -q prot.pqms
4. Create a file called opacity.ms containing the following:
molecule protein pdb4pti.cln elbow 0.5 connect protein #creates bonds protein color = grey # default, mainly carbons 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 read_surface file prot.pqms uniform_coloring green #for surface uniform_opacity 0.5 0.5 #translucent
4.Type the following command:
msdraw -i opacity.ms -r opacity.rgb
5. View the opacity.rgb image with the following command:
ipaste opacity.rgb
Last CSB Revision: Friday, 07-Feb-1997 16:44:12 EST