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Command: interfaces

Usage:
interfaces  atom-spec  [ probeRadius  rad ] [ areaCutoff  interface-area ] [ interfaceResidueAreaCutoff  res-area ]

The interfaces command calculates the buried solvent-accessible surface area (SASA) for each pair of chains in the specified set of atoms, based on chain IDs, and generates a network diagram of the interchain interfaces. Unspecified atoms are ignored, but solvent, ions, and ligand residues are NOT excluded automatically. The buried SASA is calculated as described for measure buriedArea, and results are reported in the Log. See also: clashes/contacts, hbonds, VDW radii, the ChimeraX interfaces highlight

The default probeRadius rad for calculating each SAS is 1.4 Å, often used to approximate a water molecule. Interfaces with at least interface-area buried (default 300 Å2, can be changed with the areaCutoff option) are counted as interfaces and shown as lines in the diagram. Residues with at least res-area buried (default 15 Å2, can be changed with the interfaceResidueAreaCutoff option) are considered to be interface residues.

Chain-Chain Network Diagram

1i50 'interfaces protein' diagram
In the 2D network diagram created by the interfaces command, the nodes (circles) represent chains, and the edges (lines) between nodes represent chain-chain interfaces. Node colors match the predominant colors of the chains when the diagram is created, but will toggle between that initial color when a chain is shown and gray when it is hidden. Node sizes are proportional to chain surface areas. Smaller interfaces (buried SASA less than half that of the largest interface in the structure) are indicated with dotted lines.

Clicking a node shows the atoms of the corresponding chain and any interacting chains; other nodes are grayed out and their atoms hidden. Alt-clicking a node selects the atoms of the corresponding chain. Similarly, clicking an edge shows the atoms of the two connected nodes and grays out other nodes and hides their atoms, while Alt-clicking an edge selects the atoms of the two nodes. Alt-clicking the background of the diagram clears any selection.

Most of these actions apply only to the atoms that were specified in the interfaces command; any other atoms are ignored. Showing/hiding atoms by interacting with the diagram does not affect cartoon or surface displays.

The diagram can be moved as a whole with left or middle mouse drag (initially clicking on the background) and expanded/contracted with Shift-left mouse drag. Expansion/contraction is about the point initially clicked and does not affect node sizes, only their spacing. The panel containing the diagram can be manipulated like other ChimeraX panels.

Context menus are accessed by right-clicking* various parts of the chain-chain network diagram. Most of the menu entries act on only the atoms used in the buried-area calculations, as specified in the interfaces command.

The background context menu includes:

The node context menu includes (indented entries the same as in the background context menu):

The edge context menu includes (indented entries the same as in the background context menu):

Interface Residue Plot

A plot of the chain-chain interface residues can be shown using the edge context menu in a chain-chain network diagram. The residue plot is a 2D representation of what would be obtained in 3D with Show interface (below): colored nodes (circles) for individual chain1-chain2 interface residues superimposed on a gray silhouette of the remaining residues of the second chain. The interface-residue nodes are colored to match the structure and labeled by residue number. Clicking a node selects the corresponding residue in the structure.

The plot can be moved as a whole with left or middle mouse drag (initially clicking on the background) and expanded/contracted with Shift-left mouse drag. Expansion/contraction is about the point initially clicked and does not affect node sizes, only their spacing. The panel containing the plot can be manipulated like other ChimeraX panels.

The residue plot has its own context menus, with:


UCSF Resource for Biocomputing, Visualization, and Informatics / November 2017