Make two PDB files: one with ligand and one with receptor
Type: setup grasp
Type: grasp
Click Right mouse button to get the main menu and then in the following sequence : Read |
PDB File | Show List
Select your ligand PDB file.
Click Right mouse button to get the main menu and then in the following sequence : Build |
Backbone Worm | Carbon Alpha Worm
Click Right mouse button to get the main menu and then in the following sequence: Display | Alter |Bonds | Saved Set | Rods
Type: wc=3 (Worm color equals green)
Type: ^H, Click: Shininess, Type: 50
Type: ^H, Click: Specularity, Type: 1,1,1
Click Right mouse button to get the main menu and then in the following sequence: Set Parameters | Depth Cueing | Enter New Value | Bonds, Type: 1.2
Type: a=ba,bc=0 (removes backbone atom bonds)
Type: a=ca,bc=0 (put back CA bonds)
Click Right mouse button to get the main menu and then in the following sequece: Set Parameters | System Miscellaneous | Bond Cylinnder Diameter, Type: 0.4
Click Right mouse button to get the main menu and then in the following sequece: Display | Alter | Bonds | Saved Set | Rods
Click Right mouse button to get the main menu and then in the following sequence : Read |
PDB File | Show List
Select your receptor PDB file.
Click Right mouse button to get the main menu and then in the following sequence : Formal Subsets | Make a Formal Subset | Atoms | Make All Molecules Subsets | Use this one | Use this one
Click Right mouse button to get the main menu and then in the following sequence : Formal Subsets | Fix Dials to World (so you won't accidently move ligand relative to receptor)
Click Right mouse button to get the main menu and then in the following sequence : Read | Radius/Charge File | Full.crg
Click Right mouse button to get the main menu and then in the following sequence : Calculate | A New Potential Map
Click Right mouse button to get the main menu and then in the following sequence : Set Parameters | System Miscellaneous | Minimum Surface Resolution, Type: 25
Click Right mouse button to get the main menu and then in the following sequence : Build | Molecular Surface | A Molecule | Molecule 2
Click Right mouse button to get the main menu and then in the following sequence : Display | Alter | Molecular Surface | Potential | Lit and Rendered
Click Right mouse button to get the main menu and then in the following sequence : Calculate | Pot. via Map at Surfaces | A Molecule | Molecule 2 | A constructed Surface | Surface 1
Place the cursor over the ">-<" part of the color bar and hold down the left most button until the color saturations are OK.
Type: ^B (To remove the scale)
Click Right mouse button to get the main menu and then in the following sequence : Miscellaneous | AntiAliasing (Polygons) and wait a minute.
When the picture smooths, Click Right mouse button to get the main menu and then in the following sequence : Write | RGB/Snapshot File, Type: filename.rgb