Area/Volume from Web

Area/Volume from Web uses the StrucTools server at http://molbio.info.nih.gov/structbio/basic.html to calculate surface areas and atomic Voronoi volumes from molecular coordinates. The calculated values are assigned as atom attributes. The atomic values can be summed with Attribute Calculator to produce residue areas and volumes.

The related tool Measure Volume and Area reports total surface areas and surface-enclosed volumes of molecular surfaces, GRASP surfaces, and isosurfaces from Volume Viewer and Multiscale Models (see the summary of differences).

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. Available computations are:

• Accessible Surface (Gerstein), generating an atom attribute named (by default) accessibleSurface. The method is described in:

  M. Gerstein, "A Resolution-Sensitive Procedure for Comparing Protein Surfaces and its Application to the Comparison of Antigen-Combining Sites" Acta Cryst A48:271 (1992).

• Surface Area (MSMS), generating atom attributes named (by default):
  • msmsArea_MS - the molecular or solvent-excluded surface, composed of probe contact and reentrant surface
  • msmsArea_SAS - the solvent-accessible surface, that traced by the probe center
  MSMS is described in:

  M.F. Sanner, A.J. Olson, and J.C. Spehner, "Reduced surface: an efficient way to compute molecular surfaces" Biopolymers 38:305 (1996).

• Voronoi Volume (Gerstein), generating an atom attribute named (by default) voronoiVolume. The method is described in:

  M. Gerstein, J. Tsai, and M. Levitt, "The Volume of Atoms on the Protein Surface: Calculated from Simulation, using Voronoi Polyhedra" J Mol Biol 249:955 (1995).

• Open Render/Select by Attribute - whether to open the Render/Select by Attribute tool after assigning attribute values. Even when this option is off, the attribute(s) will be available within the Render/Select by Attribute tool if it is opened 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

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 the 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 reflect any changes that have been made in Chimera (translations, rotations, deletions, bond rotations, etc.). Any solvent, ions, and other ligands not intended to be included in the calculation should be deleted from the chosen model(s) or chain(s) before initiating the calculation. All other parameters used in the calculation are determined solely by the server and are not affected by parameter settings (such as atomic radii) in Chimera.

For each attribute, the atoms are assigned the values calculated by the server (surface area in Ų, volume in ų). The number of atoms assigned values is reported in the Chimera Reply Log and status line. When the output contains data for fewer atoms than were sent to the server, possibly due to a lack of parameters, a warning message will report the number of atoms missing. 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. The atom attribute values can be summed with Attribute Calculator to produce the corresponding residue attributes.