CASTp Data

A structure and its precalculated pocket measurements can be retrieved by PDB ID (4-character Protein Data Bank Identifier) from the Computed Atlas of Surface Topography of proteins (CASTp) database using Fetch by ID or the command open (with prefix castp:).

The CASTp database does not contain all PDB entries, and structures from the database may be older versions of the current PDB entries. Results for a structure not in the database can be shown in Chimera by requesting a calculation at the CASTp server and opting for results to be returned by e-mail. After the results have been received and unzipped, opening the file named *.poc in Chimera automatically also reads files with the same name/location except the suffixes .pdb, .pocInfo, .mouth, and .mouthInfo.

CASTp information includes:

• which atoms form pockets and pocket mouths
• pocket volume and surface area
• mouth opening area and circumference

CASTp: Computed Atlas of Surface Topography of proteins. Binkowski TA, Naghibzadeh S, Liang J. Nucleic Acids Res. 2003 Jul 1;31(13):3352-5.

CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W116-8.

See also: molecular surfaces, Measure Volume and Area, Measure and Color Blobs, Surfnet, the MOLEonline Server

Each row in the dialog describes a pocket, which could be an internal cavity completely enclosed by atoms or a indentation with one or more openings to the external surface. Measurements are with respect to the molecular surface (solvent-excluded surface; probe contact + reentrant) or the solvent-accessible surface (that traced by the probe center).

Each type of measurement can be shown or hidden using the Columns menu:

• ID - pocket identifier
• MS volume - pocket volume based on the molecular surface
• SA volume - pocket volume based on the solvent-accessible surface
• pocket MS area - pocket molecular surface area
• pocket SA area - pocket solvent-accessible surface area
• # openings - number of mouths, or openings to the external molecular surface
• mouth MS area - total area of mouth opening(s) based on the molecular surface
• mouth SA area - total area of mouth opening(s) based on the solvent-accessible surface
• MS circumference sum - total circumference of mouth opening(s) based on the molecular surface
• SA circumference sum - total circumference of mouth opening(s) based on the solvent-accessible surface
• sum arc length - total length of arcs formed where two pocket atoms meet
• # corner points - number of corner points formed where three pocket atoms meet
• # triangles - total number of Delaunay triangles of mouth opening(s)

The pocket list can be sorted by the values in any displayed column by clicking the column header. Clicking the header once sorts the entries in order of increasing value and places an up arrowhead (triangle) in the header. Clicking again sorts the entries in decreasing order and places a down arrowhead (inverted triangle) in the header.

A pocket can be chosen by clicking on its line, and multiple pockets can be chosen at once. Chosen lines are highlighted in the dialog. Ctrl-click toggles the status of a line, while clicking on the first (or last) line of a contiguous block and then Shift-clicking on the last (or first) chooses all of the lines in the block.

Options for the Treatment of Chosen Pocket Atoms:

• Select - select the atoms for further actions
• Color [ color well ] (and color all other atoms [ color well ]) (factory defaults are orange and No color, respectively; using No color reveals model-level colors)
• Surface (optionally colored by hydrophobicity) - show molecular surface contributed by the atoms. The surface can be colored by amino acid hydrophobicity (values in the Kyte-Doolittle scale shown with colors ranging from dodger blue for the most hydrophilic to white at 0.0 to to orange red for the most hydrophobic), or left unchanged from its existing colors, which match the underlying atoms unless the surface has been colored separately. The first time surface is shown for a given structure, there may be a lag of several seconds as the surface is calculated.

  Only the contiguous surface patch with the largest surface area is shown. If desired, all patches associated with the pocket atoms can be shown, by selecting the atoms (using the Select option above), then using the command surface sel or Actions... Surface... show in the main Chimera menu. However, the automatically hidden patches rarely belong to the pocket of interest, instead arising when the pocket atoms also contribute to other parts of the protein surface such as neighboring pockets.

• Zoom in on - focus on the atoms and adjust view orientation
• Exclude mouth atoms - whether to omit pocket mouth atoms, if any, from the specified treatments

Hide hides the dialog without removing it; Quit removes the dialog and the structure. Help brings up this manual page in a browser window.