MSDRAW renders various atomic representations for a protein molecule. An example of two different surfaces (one clipped) together with a subset of residues is shown below:
These results were obtained for ribonuclease by the following commands:
1. Get the PDB file
getentry 2rns
2. Edit the PFB file to create three new files:
a. s.pdb containing residues 1-15
b. a.pdb containing residues 24-124
c. site.pdb containing residues 25 and 48extract pdb2rns.ent
3. Make the binary surface files *.pqms for use below:
msroll -m s.pdb -p 1.4 -q s.pqms
msroll -m a.pdb -p 1.4 -q a.pqms
4. Create a file called surf.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
#orient the whole scene
rotation -20.0 0.0 1.0 0.0
#coordinates of only residues for
# ball and stick
molecule protein site.pdb
#OBJECT - SURFACE1
#This surface file made from Ribonuclease A
read_surface a.pqms
#color outside inside cavity
component_coloring grey magenta green
#make translucent outer inner
component_opacity 1.0 0.5 1.0
#OBJECT - SURFACE2
#This surface made from ribonuclease S peptide
read_surface s.pqms
#don't clip this surface
no_clipping
#color outside inside cavity
component_coloring green green green
#make opaque
component_opacity 0.5 0.5 1.0
#OBJECT - BONDS
#make bonds (only for residues in site.pdb)
bond_radius 0.3
ball_radius 0.3
elbow 1.5 #radius at a
connect protein # creates bonds
#draw the bonds
ball_and_stick
uniform_coloring cyan
no_clipping #turn off clipping for bonds
5.Type the following command (the -z option is amount of clipping):
msdraw -i surf.ms -r surf.rgb -z 0.68
6. View the surf.rgb image with the following command:
ipaste surf.rgb
Last CSB Revision: Thursday, 13-Feb-1997 10:26:44 EST