7.3 Surface Calculation OpenGL

VEGA OpenGL can calculate and display some types of molecular surface trough its 3D engine. It's possible to display some local molecular properties like hydropathicity, lypophilicity, volume, molecular charges, etc.

7.3.1 Calculation parameters

Surface Calculation

To open this dialog, you must select Calculate -> Surface -> Calculate from the main menu. Select the type of the surface to calculate, enter the probe radius and the dot density, but remember that not all of these parameters are requested by all surface types, see the following table:

Type Description Probe Rad. Density
VdW Van der Waals
Surface accessible to solvent
Yes Yes
MEP Molecular Electrostatic Potential No Yes
MLP Molecular Lypophilic Potential No No
ILM Hydropathicity profile
(a water cluster is needed)
No Yes
PSA Polar Surface Area Yes Yes

Checking Consider selected atoms only, it's possible calculate the surface of the visible atoms only. At the end of the surface calculation, in the console you can read the area in Ų and the range of values assigned at each dot.

Uncolored surface

This is the result of a MEP calculation. Please note that the local property isn't showed as ramp of  colors. See the next section.

7.3.2 Surface coloring

To change the surface color, select from the main menu Calculate -> Surface -> Color:

Surface Color

With this dialog, you can select the coloring method by property, by atom and by color, choused with the slider or with the color table, pressing the Change button. Press OK to apply the selection or Cancel to close the window.

By property MEP surface colored by property.

By atom MEP surface colored by atom.

By color MEP surface displayed with selected color.

 

7.3.3 Saving the surface.

To save the calculated surface, select Calculate -> Surface -> Save from the main menu. The supported formats are: CSV, Quanta, Insight/Biosym, raw binary, VRML Solid and VRML dotted.

 

7.3.4 Loading the surface.

To load a pre-calculated surface, select File -> Open from the main menu. The VRML files can't be loaded.

 

7.3.5 Removing the surface.

A surface can be deleted, using the Calculate -> Surface -> Remove or Edit -> Remove -> Surface options from the main menu.