Select Contacts

Choosing Select... Contacts from the ChimeraX menu opens the Select Contacts dialog, with sections:

Chains
Atomic

Depending on the options used, the corresponding command is contacts, interfaces, or select. See also: menu Select... Zone, Contacts, Crystal Contacts, measure buriedarea, select zone, chain-chain network diagram, zone atom specification

OK performs the selection and closes the dialog, whereas Apply performs the selection without closing the dialog. Close closes the dialog without doing anything. Help shows this page in the ChimeraX browser.

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Chains

Select residues in chain-chain contact interfaces. The chains of interest should be chosen from the respective lists: one or more reference chains from the list on the left, and from the right, one or more chains that may be in contact with the reference chain(s). Options:

• Select contacts in [which set] of chains – whether to select the identified residues in only the lefthand set of chosen chains or in both sets of chosen chains (default)
• Select residues with:
  • buried solvent-accessible surface area ≥ [area] Ų – residues found to bury at least area of solvent-accessible surface (default 15.0 Ų) in the interface between a chain chosen on the left and a chain chosen on the right, with no restriction on the size of the chain-chain interface (the interfaces areaCutoff criterion is set to 0.0 Ų)
    – OR –
  • atomic distance ≤ [dist] Å – select residues with at least one atom within dist (default 3.5 Å) of an atom in the other chain

For either type of calculation (buried surface areas or distances), only atoms in protein and nucleic acid chains are considered, not ligands, ions, or solvent. To identify contacts of those other types of residues, use the Atomic section instead.

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Atomic

Select atomic contacts of the current selection based on either the VDW overlap or the distance between atomic centers, with additional options to limit the scope of selection (details...) and to show the full Contacts tool.