Surface calculation

8.5 Surface calculation

VEGA ZZ can calculate and display some types of molecular surface. It's possible to display some local molecular properties like hydropathicity, lypophilicity, volume, molecular charges, etc.
VEGA ZZ uses two methods to generate the surfaces. For dotted surfaces, it uses the fast double cubic lattice method implemented in the NSC approach (F. Eisenhaber, P. Lijnzaad, P. Argos, C. Sander, and M. Scharf, J. Comput. Chem, Vol. 16 N3, 273-284, 1995). For solid and mesh surfaces, it uses a method named marching cubes implemented in the source code provided by Paul Bourke (for more information, click here) and it's based on the surface facet approximation to an isosurface through a scalar field sampled on a rectangular 3D grid.
The surface properties (DEEP, ILM, MEP, MLP and PSA) are calculated for each dot with the appropriate algorithm.

The DEEP algorithm is very simple: for each dot is calculated its distance from the geometric center of the molecule. This property is useful to color the surface by gradient in order to highlight the deep pockets and the cavities of the molecule.

The ILM method is based on the principle that at equilibrium the solvent molecules will be more probably found near the hydrophilic regions of the solute, while they will be repelled by the more hydrophobic moieties. The method allows the calculation of a global hydropathicity index (ILM) and this property can be also projected on the molecular surface, giving rise to a very detailed local hydropathicity mapping. The computational steps required for the ILM calculation are:

1) solvation of the molecule using a water cluster (see the solvent cluster section);
2) molecular dynamics (T= 300K, time step = 1 fs). The simulation length is must be tuned on the basis of the system complexity;
3) ILM calculation.

The equation used to calculate the ILM property is:

ILM equation

where: d_ij is the distance between the the solute atom i and the mass center of the water molecule j, n_a is the number of the solute atoms and n_s is the number of water molecules (A. Pedretti, A.M. Villa, L. Villa, G. Vistoli, Internet Journal of Chemistry, Vol. 45 (7), Art. 13, 2000).

The Molecular Electrostatic Potential (MEP) surface is calculated projecting the atomic charges on the molecule surface. The value of each i surface dot is calculated by the following equation:

MEP equation

Where:
V_i	=	projected value on the i surface dot.
Q_j	=	partial charge of the j atom.
d_ij	=	distance between the i dot and j atom.

The Molecular Lipophilicity Potential (MLP) is calculated projecting the Broto-Moreau lipophilicity atomic constants on the molecular surface (P. Gaillard, P.A. Carrupt, B. Testa, A. Boudon, J. C.A.M.D., Vol. 8, 83, 1994).

The Polar Surface Area (PSA) is calculated considering polar and apolar atom surfaces. Apolar atoms are C and H bonded to C. Polar atoms are O, S, N, P and H not bonded to C. These properties are projected on the surfaces using two color codes: blue (apolar surface) and red (polar surface).

8.5.1 Surface management

New To manage surfaces, you must select Calculate Surface Calculate in main menu. VEGA ZZ can manage more than one surface with independent properties and visualization parameters. The first box at top is the list of surfaces in the current workspace. There are no limits of surface dimensions, number of dots and number of surfaces. By the context menu, you can perform basic operations as show/hide, rename and remove the surfaces. If you want to apply any change to more than one surface, a multiple selection is required and it must be done holding down shift or control (Ctrl) keys when you click the list. The six buttons below the surface list allow to remove a single surface (Remove) or all surfaces (Remove all), to show or hide all surfaces at once (Show all and Hide all), to load or save surface files (Load and Save). The surfaces file format writable by VEGA ZZ are: Comma Separated Values (*.csv), IFF (*.iff), Insight (*.srf), Quanta (*.srf) and Raw binary (*.raw). You must remember that to load a surface, you could use also File Open main menu item and when you save the molecule in IFF format, all surfaces are saved in the same fie too.
Another way to switch between show/hide status is to double click the surface in the list.
Drag & dropping the items in the list, you change not only the surface order but also the rendering sequence. If you have two transparent surfaces of the same molecule, one inside the other, the inner one must rendered at first time and thus it must be in the first position of the list in order to respect the OpenGL priorities.

8.5.1 Surface calculation

In New tab of Surface management window, there are the controls to calculate a new surface. In the top-right box, you can choose the shape type (Dots, Mesh and Solid), the Type of surface (see the following table), the probe radius (Probe Rad. field) and the surface dot density (Density field). This last field could be replaced by Mesh size, if you select Mesh or Solid surface shape. The probe radius can't be changed for all surface property types.

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

Checking Consider selected atoms only, it's possible calculate the surface of visible atoms only. After the surface calculation, in the console, you can read the area in Ų and the range of values assigned to each point. If you want to color the surface by property using a color gradient, you must check the Color by gradient option (see the surface gradient section).

		Dotted surface
Mesh surface
		Solid surface
Multiple solid sufaces

8.5.2 Surface color

Color The Color tab of Surface management window allows to change surface color. The surface can be colored by Atom, Residue, Chain, Segment, Molecule and Surface number, using the same color codes applied to atoms. Selecting Custom as color method, you can choose the color for the surface. Click Apply button to change the surface color.

		Color by atom
Color by residue
		Color by chain
Color by segment

8.5.3 Surface transparency

In Transparency tab ,you can enable/disable the surface transparency and its intensity (0 = full transparent, 255 = full opaque). The default value is 128. The Use OpenGL list checkbox enables the use of OpenGL list for faster surface rendering, but the feed-back speed go down (e.g. changing the color, the transparency, etc). This rendering mode isn't required if you have an high-end OpenGL graphic card. If your graphic card is OpenGL 1.5 compliant, this label is changed to Use vertex buffer and it's automatically enabled at the first VEGA ZZ run. This rendering mode stores the surface in the high speed memory of the graphic card increasing dramatically the rendering speed (at least 2 time faster).
By the Dot size slider you can change the dot size of a dotted surface. When you select values greater than four, the dots are converted to small spheres.

		Transparent surface
Dotted surface with small spheres

8.5.4 Surface gradient

When you calculate a surface property (DEEP, ILM, MEP, MLP and PSA), you can color each dot by a color ramp (gradient) in which the first color and the last colors are the boundaries of the property range. In Gradient tab, you can set the number of color nodes defining the gradient (from 2 to 6). They can be changed by color mixer, clicking the small boxes above the gradient bar. The color nodes can be shifted to left or right clicking < and > buttons. Activating the context menu (use the right mouse button on the gradient bar), you cant perform the same operation selecting Shift left and Shift right. Invert inverts the order of the color nodes from left right to right left. The Preset submenu contains the preset color gradients saved in ...\VEGA ZZ\Config\glgrad file (click here for more information about the file format).
Auto range checkbox indicates to VEGA ZZ to assign the boundaries of the property range to the extremities of the color gradient. If you want surfaces with comparable color ramps, you must disable this function and specify manually the property range that must be equal for all surfaces. In this way, dots with same colors of different surfaces have the same property value. Fill range button helps you to define manually the property range filling the range with the highest and the lowest property values. This is the same operation performed when Auto range is checked but in this way you can adjust the range. Apply button applies the gradient to the surfaces selected in the list. The gradient is automatically used if Color by gradient is checked in New tab when you calculate a new surface (see the surface calculation section).

8.5.5 Default settings

In Settings tab, you can change the default settings used when you calculate a new surface. You can preset the surface color, the use of the OpenGL lists or the vertex buffer (see above), the surface transparency, the transparency value and the surface dot size. To revert to the pre-defined parameters, you must click Default.