The above is a surface model of lyzozyme with the surface made transparent and the sidechains displayed as lines colored according to polarity.

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 atoms of sidechains red)

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

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

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

Type: r=-wat

Click Right mouse button to get the main menu and then in the following sequence: Display | Alter | Molecular Surface | Discrete Colors | Transparent

Last Modified: Thursday, 04-Dec-1997 14:40:10 EST