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Molecular Surface Panel |
The Molecular Surface Panel is used to generate a surface that follows the molecular surface but is smoother than the CPK surface. The best known type is the Connolly surface. Imagine rolling a ball over the assembly of spheres constituting the vdW surface. Where the outside of the ball contacts the vdW spheres, the surfaces coincide. But where two vdW spheres come together, the Connolly surface follows the surface of the solvent sphere, giving fillets rather than cusps where the vdW spheres intersect. True Connolly surfaces are very expensive to generate, in general; therefore often an approximation is used. Note that changing the solvent sphere or probe radius affects the size and shape of the surface.
To open the Molecular Surface panel, you can:
Choose Workspace → Surface → Molecular Surface in the main window.
The standard picking controls in the Atoms for surface display section are used to select the atoms for which the surface is displayed. The surface is generated for the atoms specified in the Surface Context section. For example, if you select atom number 1 for surface display and choose Entry for the surface context, a surface for the entire entry in which atom 1 resides will be generated, but only the part of the surface that "belongs" to atom 1 will be displayed.
The options on the Surface context option menu determine which atoms are used to generate the surface. For the atoms chosen in the Atoms for surface display section, you can generate a surface for the entry or the molecule that they belong to, or just for the selected atoms (the default). If the entry or the molecule contains more atoms than were chosen for surface display, the displayed surface will be a partial surface.
The surface is created using interpolation on a cubic grid. This option menu allows you to specify the resolution of the resulting surface. Higher resolution means a smoother surface, which is slower to generate and draw. Lower resolution means a rougher surface but is faster to generate and and draw (and hence rotating will be faster). These controls affect the grid spacing for the surface. When you select Low, Medium, or High, the grid spacing in angstroms is displayed in the text box. If you want to specify the grid spacing, choose Custom and enter the desired value in the text box.
This text box specifies the radius of the probe that is to be rolled over the van der Waals surface. The default solvent sphere or probe radius of 1.4 Å corresponds to water.
Specify the scaling factor for the van der Waals radius.
Molecular surfaces can be created as a composite of two surfaces, by performing a Boolean operation on the corresponding volumes. The available operations can be chosen from this option menu:
When you choose an option other than None, a standard set of picking controls labeled Atoms for surface boolean operation is displayed below the option menu, which you can use to select the atoms for the second surface.
This button starts the molecular surface generation process using the settings from this panel. During this time Maestro is inoperative and no user interaction is possible. Large-sized surfaces or surfaces with fine grid spacing can take some time to generate.
In the ball-rolling description of an extended surface, the locus of points described by the surface of the probe sphere closest to the molecular system constitutes the molecular surface. The molecular surface follows the van der Waals surface except where the surfaces of two atomic spheres are closer together than a probe diameter. In such regions (termed "re-entrant"), the molecular surface is bridged over by a surface section that follows the probe surface. The concept of molecular surface is usually associated with Connolly (M.L. Connolly (1983) "Analytical molecular surface calculation", J. Appl. Crystallogr. 16, 548-558). However, Maestro does not use Connolly's algorithm for producing the molecular surface.
The method used by Maestro to create the molecular surface is an elaboration of what is sometimes called the "ink-blot" method. In the ink-blot method, the volume enclosed by the extended surface is first constructed. Then any points within this volume that lie interior to the generating solvent probe are declared to be external. After this process is complete, the boundary of the remaining internal volume is the molecular surface.
Maestro first sets up the grid for the extended surface and interpolates within it to produce the extended surface, as in the extended-surface algorithm described above. Recall that interior grid points have values less then unity and exterior points have values greater than unity. These values are reset so that exterior points are given a value of zero and interior points are given a value much greater than unity. Then a probe sphere is placed on each vertex of the extended surface in turn. For each placement, for all grid vertices in the probe sphere's minimal enclosing grid cube, the grid vertices are given the value Min(d/r, previous_value). Outside the extended surface, the value will always remain zero. Inside the extended surface, the value will rise from near zero close to the probe center to somewhat greater than unity at the grid cube boundaries. The vertices of the molecular surface are then created by interpolation to unity on the grid.
The molecular surface appears from the outside to closely resemble the van der Waals surface, since it follows the van der Waals surface, except for the bridging re-entrant portions. We mentioned earlier that interior atoms of an extended surface are buried (have no surface points on their atomic spheres), but that few, if any, atoms are buried in this sense for a van der Waals surface. Atoms that are buried in an extended surface will also be buried in a molecular surface, since no atomic sphere will have molecular surface points on it unless the atom is adjacent to a region in which a probe molecule will fit. Thus, in their tendency to bury atoms, molecular surfaces resemble extended surfaces rather than van der Waals surfaces.
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