MSDRAW renders various atomic representations for a protein molecule. An example of a backbone worm with a translucent surface and internal cavity 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 component.ms containing the following:
#GENERAL COMMANDS #orient the light source (must be first line, if used) light_source 0.5 0.5 1.0 #Give values for # depth ambient diffuse specular exponent # (The first four must = 1.0) # depth = depth cueing # ambient = brightness at rear # diffuse = amount of dullness # specular = amount of shininess # exponent = " " " shading_model 0.5 0.0 0.3 0.2 20.0 #MOLECULE COMMANDS #orient the whole scene rotation 20.0 0.0 1.0 0.0 #define the molecule molecule protein pdb4pti.cln #FIRST OBJECT - BONDS #make bonds bond_radius 0.3 ball_radius 0.3 elbow 2.0 # connect protein # creates bonds #designate color of bonds protein color = white oxygens = atom matches O oxygens color = red nitrogens = atom matches N nitrogens color = blue sulfurs = atom matches S sulfurs color = yellow #draw the bonds ball_and_stick atom_coloring # use colors specified above no_clipping #turn off clipping for bonds #SECOND OBJECT - SURFACE #make the surface and clip according to # -z command option read_surface prot.pqms #color outside inside and cavity component_coloring grey magenta green #make translucent outer inner cavity surfaces component_opacity 1.0 0.5 1.0
5.Type the following command (the -z option is amount of clipping):
msdraw -i component.ms -r component.rgb -z 0.3
6. View the component.rgb image with the following command:
ipaste component.rgb
Last CSB Revision: Friday, 07-Feb-1997 16:44:22 EST