8.5 Surface calculation
VEGA ZZ 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.
VEGA 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
called 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) Solvatation 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 in
function of the system complexity and please remember that the solvent-solute
environment will be at the equilibrium.
3) ILM calculation.
The equation used to calculate the ILM
property is the following:

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 charge on the
surface. The value of each i surface dot is calculated with the following
equation:

Where: |
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 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
To
manage the surfaces, you must select Calculate
-> Surface -> Calculate from the main menu. VEGA ZZ can manage more
than one surfaces with independent properties and visualization
parameters. The first box at top, indicates the surfaces in the current
workspace. No limits are present about the surface dimensions, number of
dots and number of surfaces. Thanks to the context menu, it's possible to
perform basic operations as show/hide, rename and remove the
surface. If you want apply that operation to more than one surface,
a multiple selection is required and it must be done holding down the
shift or the control (Ctrl) keyboard buttons when you click the list with
the left mouse button. The six buttons below the surface list allow to
remove one surface (Remove) or all surfaces (Remove all), to
show or hide all surfaces at once (Show all and Hide all),
to load or save a surface file (Load and Save). The surface
file format writable by VEGA ZZ are: Comma Separated Values (*.csv), IFF
(*.iff), Insight (*.srf), Quanta (*.srf) and Raw binary (*.raw). Please
remember that to load a surface, you could use the 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 the show/hide status is to double click to
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 the New tab of the Surface
management window, are placed the controls to calculate a new surface. In
the top-right box, you can choose the shape type (Dots, Mesh and Solid)
and use the Type field to select the surface type (see the following
table), the Probe Rad. field to enter the probe radius and the Density
field to enter the surface dot density. This last field could be replaced by the
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 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
point. If you want 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
The
Color tab of the 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 the atoms. Selecting Custom as color method,
it's possible to color the surface choosing a custom color. Click the Apply
button to paint the surface. |
 |
|
Color by atom |
Color by residue |
|
 |
 |
|
Color by chain |
Color by segment |
|
 |
8.5.3 Surface transparency
In
the 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 dramatically increasing 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
in 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 using a color ramp (gradient) in which the first color and the
last colors are the boundaries of the property range. In the Gradient
tab, you can set the number of color nodes defining the gradient (from 2
to 6). They can be changed with the color mixer, clicking the small boxes above the gradient
bar. The color nodes can be shifted to left or right clicking the <
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. The Invert item
invert the order of the color nodes from left -> right to right ->
left. The Preset submenu contains the preset color gradients saved
in the Data\glgrad file (click here
for more information about the file format).
The 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 ramp, 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 but in different surfaces have got the same property
value. The Fill range button help you to define manually the
property range filling the range with the highest and the lowest property
value. This is the same operation performed when Auto range is
checked but in this way you can adjust the range. The Apply button
applies the gradient to the surfaces selected in the list. The gradient is
automatically used if Color by gradient is checked in the New
tab when you calculate a new surface (see the surface
calculation section). |
8.5.5 Default settings
In
the 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
the Default button. |