RELACIONES CON PRINCIPIOS DEL ESTADO

From theSurfacessubmenu of theDisplaymenu in the main menu bar, you can generate three kinds of surfaces that have similar characteristics: molecular surfaces (Connolly surfaces), van der Waals surfaces, and extended radius surfaces.

Surfaces can only be generated for project entries. If you try to generate a surface for the scratch entry, you will be prompted to create a project entry from the scratch entry. Each surface is associated with only one entry, but an entry may have zero or more surfaces.

11.1.1

Surface Generation Controls

Most of the surface-generation settings are common to the Molecular Surface panel, the

Extended Radius Surface panel, and the VDW Surfacepanel. All the settings are discussed below.

Name

You can name the surface by entering the name in theNametext box. If an entry has more than one surface, each surface name for that entry must be unique.

Atoms for surface display

The surface is displayed only for the atoms specified in theAtoms For Surface Displaysection of the panel. You can select atoms by picking in the Workspace, by entering an ASL expression in theASLtext box, by clickingAll, or by clickingSelectand using theAtom Selectiondialog box. If you want to reset the atom selection, clickClear. If you haveShow Markersselected, the atoms you select are marked in the Workspace.

Boolean operation

In theMolecular Surfacepanel, you can create surfaces that are formed by Boolean operations on two surfaces. The operations are:

• None—Create a single surface. This is the default.

• Union—Create a surface that encloses the volume occupied by either of the two surfaces (Boolean OR).

• Intersection—Create a surface that encloses the common volume of the two sur- faces(Boolean AND).

• Difference—Create a surface that encloses the volumes that are unique to each sur- face(Boolean XOR).

The atoms for the second surface are specified in the Atoms for surface boolean operation

section. The controls are the same as in theAtoms for surface display section.

Surface context

The surface is actually generated for the atoms specified in theSurface contextsection, but only the portion of the surface defined by theAtoms for surface displayis displayed. If you chooseEntryor Molecule, the surface is generated for the entries or molecules of which the atoms selected for surface display are a part. If you choose Selected atoms, the surface is generated only for the atoms selected for surface display, and appears as a complete surface. You can also limit the surface dynamically once it is created, using theLimit Surfacedialog box. SeeSection 11.4.1 on page 173 for details.

Image quality

In theMolecular Surfacepanel you can set the quality of the image toLow,Medium, orHigh. These controls set the grid spacing for surface generation. You can also selectCustomand enter a grid spacing in the text box. The grid spacing values for the other three choices are displayed in this text box. The high quality surface is smoother but takes longer to generate.

Probe radius

This setting appears only on theMolecular Surface panel and theExtended Radius Surface

panel. Since the van der Waals surface is, by definition, built directly on the van der Waals spheres, a probe radius setting is not needed for this panel.

The value in theProbe Radiustext box controls the radius of the probe sphere that is “rolled over” the van der Waals surface of the molecule. The default probe radius of 1.4 Å corresponds to water.

Create Surface

To start the surface generation, clickCreate Surface. During this time Maestro is inoperative and no user interaction is possible. For large surfaces and high quality, surface generation can be time consuming.

11.1.2

Molecular Surfaces

In theMolecular Surfacepanel, you can generate a surface that follows the molecular surface, but is smoother than the CPK surface. The best known type of molecular surface is the Connolly surface. Imagine rolling a ball, representing a solvent molecule, over the assembly of spheres constituting the van der Waals surface. Where the outside of the ball contacts the van der Waals spheres, the surfaces coincide. Where two van der Waals spheres intersect, the Connolly surface follows the surface of the solvent sphere, producing fillets rather than cusps. Changing the solvent sphere or probe radius affects the size and shape of the surface. Reducing the grid spacing improves the accuracy of the surface, but increases the calculation time. You can also generate a surface by performing a Boolean operation on two surfaces—see the previous section for details on how to do this.

To open theMolecular Surfacepanel, chooseMolecular Surfacefrom theSurfacessubmenu of the Display menu. Instructions for using the settings in the Molecular Surface panel are described inSection 11.1.1 on page 163.

11.1.3

Extended Radius Surfaces

In the Extended Radius Surfacepanel, you can generate a surface constructed on van der Waals spheres in a similar way to a Connolly surface. In an extended radius surface, the point that corresponds to the center of the probe is used to generate the surface, rather than the point representing the closest contact of the probe with the surface. An extended radius surface therefore shows roughly the surface that the centroid of a solvent or a ligand cannot penetrate. Thus, looking at bound ligands with wire bond representation, the ligands would “hug” but not penetrate the extended-radius surface.

Figure 11.1. The Molecular Surface panel.

To open the Extended Radius Surface panel, choose Extended Radius from the Surfaces

submenu of the Display menu. Instructions for using the settings in the Extended Radius Surface panel are described inSection 11.1.1 on page 163.

Figure 11.3. The VDW Surface panel.

11.1.4

van der Waals Surfaces

TheVDW Surfacepanel is used to generate a van der Waals surface. This surface is identical to the CPK molecular representation with the percentage set to 100.

To open the VDW Surfacepanel, choosevan der Waals from theSurfaces submenu of the

Displaymenu. Instructions for using the settings in theVDW Surface panel are described in

Section 11.1.1 on page 163.