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:
where: dij is the distance between the the solute atom i and the mass center of the water molecule j, na is the number of the solute atoms and ns 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:
|Vi||=||projected value on the i surface dot.|
|Qj||=||partial charge of the j atom.|
|dij||=||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
manage surfaces, you must select 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
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
main menu item and when you save the molecule in IFF format, all surfaces
are saved in the same fie too.
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.
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).
|Multiple solid sufaces|
8.5.2 Surface 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
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).
|Dotted surface with small spheres|
8.5.4 Surface gradient
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).
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.