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Tool: Clashes, Contacts

Clashes and Contacts are two separate tools with nearly identical options. Some of the default parameters are different, as meant to detect:

The corresponding commands are clashes and contacts. See also: Rotamers, H-Bonds, Distances, Crystal Contacts, interfaces, select by pseudobond length, measurements, Protein-Ligand Binding Sites tutorial

Clashes and Contacts can be opened from the Structure Analysis section of the Tools menu and manipulated like other panels (more...). Clicking Apply (or OK, which also dismisses the dialog) runs the calculation. Several of the dialog settings are remembered as preferences when the calculation is run. Clicking Reset restores the dialog to factory default settings.

Interaction parameters:

Treatment of results:

Write information to: Where to write clash/contact information, including atom pair specifications (see the Labels preferences for specifier style), overlaps, and center-center distances; disallowed with continuous monitoring.

Frequency of checking:


UCSF Resource for Biocomputing, Visualization, and Informatics / March 2021