Area/Volume from Web Area/Volume icon

Area/Volume from Web uses the StrucTools server to calculate atomic surface areas and Voronoi volumes from molecular coordinates. The calculated values are assigned as atom attributes. See also: Measure Volume and Area, CASTp Data, surface, measure buriedArea

Note that when a molecular surface is generated in Chimera, the total analytical solvent-accessible and solvent-excluded areas are automatically reported in the Reply Log, and the values per atom and residue are assigned as attributes named areaSAS and areaSES. These values correspond directly to the molecular surface in Chimera and depend on the same parameters (VDW radii and various molecular surface settings). By contrast, only the settings in the Area/Volume from Web dialog are sent to the StrucTools server, and other parameters such as VDW radii are determined solely by the process underlying the server.

There are several ways to start Area/Volume from Web, a tool in the Surface/Binding Analysis category. In the resulting dialog, one or more molecule models can be chosen from the Molecules list, or chains from the Chains list.

Calculation options:

Different attribute names can be specified, keeping in mind that an attribute name should be an alphanumeric string without spaces (although underscores are allowed), should not begin with a digit, underscore, or capital letter, and should not be the same as the name of a built-in attribute.

Further options:

OK initiates the calculation and dismisses the dialog, whereas Apply initiates the calculation without dismissing the dialog. Close dismisses the dialog, and Help opens this manual page in a browser window.

The transformed coordinates of atoms in the chosen model(s) or chain(s) are sent to the StrucTools server, where they are handled collectively. For example, if proteins in two different models are positioned to form a complex, the results obtained for each protein when both models are chosen will differ from the results obtained for each protein separately. The coordinates will include modifications made in Chimera, such as bond rotations. However, other inputs such as atomic and probe radii are determined only by the server and the settings in the Area/Volume from Web dialog. The atomic radii and molecular surface settings in Chimera are not used.

For each attribute, the atoms are assigned the values calculated by the server (surface area in Å2, volume in Å3). The total area or volume and the number of atoms assigned values are reported in the Reply Log and status line. When the output contains data for fewer atoms than were sent to the server, a warning message will report the number of “missing” values. This is quite common and rarely a cause for concern; for example, if the No Hetatms option is chosen, there will be no output for such atoms. Atoms missing from the server output will not be assigned attribute values, and atoms with uncalculatable Voronoi volumes will not be assigned a volume value. Attribute values can be summed over sets of atoms with the Attribute Calculator.

UCSF Computer Graphics Laboratory / March 2014