Find Clashes/Contacts Find Clashes/Contacts icon

Find Clashes example Find Clashes/Contacts identifies interatomic clashes and contacts based on VDW radii and user-specified criteria. Terminology:

During continuous monitoring, such interactions can be shown with selection, coloring, and pseudobonds. Discontinuous monitoring additionally allows writing out information and assigning the largest overlap per atom as an attribute named overlap. See also: FindHBond, Intersurf, Rotamers, RR Distance Maps, Crystal Contacts

There are several ways to start Find Clashes/Contacts, a tool in the Structure Analysis and Surface/Binding Analysis categories. It is also implemented as the command findclash.

Atoms to Check are specified by selecting atoms, clicking Designate, and indicating which interactions should be found:

Interactions between atoms in different submodels of the same model are ignored (note the findclash command has an option to include such interactions, however). Changing the selection will not automatically change any designated sets.

The Clash/Contact Parameters control what will be considered a clash or contact. The overlap between two atoms is defined as the sum of their VDW radii minus the distance between them and minus an allowance for potentially hydrogen-bonded pairs:

overlapij = rVDWi + rVDWj – dijallowanceij
Options for the Treatment of Clash/Contact Atoms: Options for the Frequency of Checking:

UCSF Computer Graphics Laboratory / September 2014