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VDW Surface Panel |
The VDW Surface Panel is used to generate a van der Waals surface. The van der Waals surface is the outer surface of the collection of atomic spheres for each atom in the molecule. Portions of atomic sphere surfaces that lie within other spheres are not part of the surface. The radius of each atomic sphere is the van der Waals radius of the atom.
To open the VDW Surface panel, you can:
Choose Workspace → Surface → Van der Waals 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, 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 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.
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