December 07, 2017
How to get the hydrophobicity through Chem3D Surface calculation?
Please try the following prior to select the "Color Mapping"
1. Go to Surfaces>Advanced Molecular Surfaces.
2. Select the surface type and what you want to include and exclude in the Advanced Molecular Surfaces dialog box.
Solvent atoms are excluded by default but may be included with the check box. Hidden atoms (usually hydrogens)may also be included or excluded. After displaying a surface, you can set surface transparency and reflectivity. You can color the surface by atom, element, or group color, or by group hydrophobicity, in addition to monochromatic surfaces of any color. You can also restrict the surface either by distance from the selected group, or by flooding.
If you are trying to get the hydrophobicity of peptides then try the Connolly molecular surface.,
After performing the calculation select Connolly Molecular Surface and then select Group Hydrophobicity from the Color Mapping