Color a molecular surface by electrostatic potential

1. Launch Grasp
• Use right mouse button to select command options
• From menu, select "Read:PDB File:Enter File Name:"
• The text window will pop forward, type .pdb file name, with full directory path
• You should then see a stick drawing of your molecule, with the unit cell axis shown.
2. Assign charges, "Read: Radius/Charge File (+Assing):full.crg"
3. Calculate the potential map, "Calculate: New Potential Map"
4. Constuct molecular surface, "Build: Molecular Surface:All atoms"
5. After the white molecular surface appears, change the display mode, "Display: Alter: Molecular Surface: (Color Surface by): (Surface Display Mode)"
• Options in "()" mean accept the default. Click the mouse off the menu.
• You shouldn't see a change in the display yet.
6. Calculate potential values of all atoms, "Calculate: Pot. via Map at Surfaces/Atoms:All Atoms:All Surfaces"
• Colors will probably be faint.
• Toggle the ">-<" part of the color scale bar to decrease the right and left numbers until the desired contrast level is obtained (usually between `0 and 20 in absolute values).

Display surface potential and curvature side by sided

• Calculate the curvature, "Calculate: Surface Curvature (+Display): All Surfaces: All Atoms"
• This takes awhile, wait until the displayed map turns green and grey
• Change to split screen mode, "Display: Stereo/Split ON: Dials to Both"
• You should see two green/grey images.
• With the bottom right dial, move the two surfaces apart, if necessary.
• Scale with the right dial button above the separation dial.
• Change the left surface to potential, "Display: Alter: Molecular Surface: Potential: (Surface Display Mode):Left"