Area/Volume from Web

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:

• Accessible Surface (Gerstein) [details at StrucTools]
  
  
  • Surface probe size (1.3/1.4/1.5/1.6)
  • Atoms to use (No Hetatms/Atoms + Hetatms/All atoms except waters)
    *hydrogens are ignored
  
  generates atom attribute accessibleSurface (default name)
  
  
• Surface Area (MSMS) [details at StrucTools]
  
  
  • Surface probe size (1.3/1.4/1.5/1.6)
  • Atoms to use (No Hetatms/Atoms + Hetatms/All atoms except waters)
  
  generates atom attributes with default names msmsArea_MS (solvent-excluded surface area) and msmsArea_SAS (solvent-accessible surface area)
  
  
• Voronoi Volume (Gerstein) [details at StrucTools]
  
  
  • Method (Normal Voronoi/Method B/Radical Plane/Modified Method B)
  • Radii (Chothia Radii/Richards Radii)
  • Atoms to use (No Hetatms/Atoms + Hetatms/All atoms except waters)
    *hydrogens are ignored
  
  generates atom attribute voronoiVolume (default name)

Further options:

• Open Render/Select by Attribute - whether to start Render/Select by Attribute, which shows a histogram of attribute values and allows mapping them to color or using them as selection criteria. The atomic values and totals per residue will be listed automatically in the dialog as atom and residue attributes, respectively. Even if this option is not used, the attribute(s) will still be available in Render/Select by Attribute if it is started later in the session.
• Save server output to file - whether to save the HTML output from the server as a file
• Show server output in browser - whether to show the HTML output 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 Ų, volume in ų). 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.