The above is a surface model of lyzozyme with the surface colored according to the polarity of the residues.

It was made by the following steps.

Obtain a protein PDB file using getentry or other source.

Change the filename extension to ".pdb"

Type:

setup grasp

and

grasp

or: source /sgi/local/bin/grasp.set and grasp

Click Right mouse button to get the main menu and then in the following sequence : READ | PDB File | Show List

Select your PDB file.

With the cursor initially in the black box type, in sequence:

bc=1 (Colors everything white)

bc=2,a=sch (Colors bonds of sidechains red)

bc=4,r=pol,a=sch (Colors polar sidechain bonds blue)

bc=7,r=hyd,a=sch (Colors hydrophobic sidechain bonds yellow)

Click Right mouse button to get the main menu and then in the following sequence : Build | Molecular Surface | Enter String

In the box that opens up, type: r=-wat (Exclude water from the surface calculation) and hit return.

A plain white molecular surface will be drawn around non-water atoms.

Move the cursor back into the black box and type: c=b (color atoms same as bonds)

Type: vc=a (Surface vertex color same as respective atom)