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Extended Radius Surface Panel |
The Extended Radius Surface panel is used to generate a surface similar to the van der Waals surface, but with an extended radius. The surface is the outer surface of the collection of atomic spheres with a radius equal to the sum of the van der Waals radius and a probe radius.
To open the Extended Radius Surface panel, you can:
Choose Workspace → Surface → Extended Radius in the main window.
To create a surface, select atoms for the displayed portion of the surface using the tools in the Atoms For Surface Display section, select a Surface Context option to determine the full surface that is to be generated, enter a probe radius, then click Create Surface.
While surface creation is in progress no other tasks can be performed.
Surfaces can only be generated and associated with project entries. The Scratch Entry cannot be used to create a surface.
Each surface is associated with only one entry. An entry may have zero or more surfaces. If it has more than one surface, each surface name must be unique. A project may have duplicate surface names as long as the surface names associated with any single entry do not contain duplicates.
Select the atoms for which the surface is to be displayed with the standard picking controls in this section. 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 is generated, but only the part of the surface that "belongs" to atom 1 is 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.
Specify the radius of the probe that is to be added to the van der Waals radius. The default solvent sphere or probe radius of 1.4 Å corresponds to water. The generated surface depends on the value entered in this text box.
Specify the scaling factor for the van der Waals radius.
Clicking Create Surface starts the surface generation process using the settings from this panel. During the surface generation, Maestro is unavailable for any user interaction.
An extended radius surface shows roughly the surface that the center of a ligand atom with the given probe radius cannot penetrate. Thus, looking at bound ligands with the wire bond representation, the ligands would "hug" but not penetrate the extended-radius surface.
If the probe radius is the size of a solvent molecule, the extended surface is the solvent-accessible surface. The default probe radius, 1.4 Å is conventionally used for the radius of a water molecule. Thus, by default, Maestro's extended surface is the solvent-accessible surface in water solution. The concept of solvent-accessible surface is set out in Lee, B. and Richards, F.M. (1971). "The Interpretation of Protein Structures: Estimation of Static Accessibility", J. Mol. Biol. 55, 379-400.
For small molecules, the extended surface has a greater area than the van der Waals surface, since the atomic spheres are larger for extended surfaces. However, for large, packed molecules, like proteins, the van der Waals surface has the larger surface area. This is because, except for atoms directly bonded together (or, to some extent, in 1-3 disposition), the atomic spheres in a van der Waals surface do not significantly overlap. Thus, a significant portion of the van der Waals surface of a protein is associated with atoms in the interior. However, when the spheres become larger, as they do with extended surfaces, the interior atoms become buried and do not contribute to the surface. In other words, substantial portions of a protein's van der Waals surface lie inside the protein, whereas this is not true for the extended surface, at least with the default 1.4 Å probe radius.
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