CASTp Data

1ovh pockets

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:

based on Delaunay triangulation, alpha shape, and discrete flow calculations [details at the CASTp site]. References:
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.
Retrieving/opening CASTp results in Chimera shows the structure in the main graphics window and associated data in a dialog, or Pocket List. CASTp information is included in saved sessions.

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

CASTp Pocket List

1ovh pocket list

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:

Column display settings are saved in the preferences file and used for subsequently retrieved CASTp data. If the pocket list is hidden or obscured by other windows, it can be raised using its instance in the Tools menu.

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:

Option settings are saved in the preferences file and used for subsequently retrieved CASTp data.

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

UCSF Computer Graphics Laboratory / August 2019