The above is a model of lyzozyme with the internal cavities displayed and colored according to the polority of the residues surronding the cavity.

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

Type: r=-wat (Exclude water from the surface calculation)

Type: c=b (Color atoms same as bonds)

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

Click Right mouse button to get the main menu and then in the following sequence: Build | Cavities/Connectivities

Type: vc=0,V=1 (Make the main surface "V" invisible)

Click Right mouse button to get the main menu and then in the following sequence: Miscellaneous | Invert Normals