Find Clashes/Contacts Find Clashes/Contacts icon

Find Clashes example Find Clashes/Contacts identifies clashes and/or contacts between atoms, based on VDW radii and user-specified criteria. 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, 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 the desired set of atoms, clicking Designate, and indicating whether to check the atoms against themselves or against all other atoms (default). That set of atoms will remain designated for clash/contact detection regardless of any subsequent changes in the selection.

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 Frequency of Checking: Settings under Treatment of Clash/Contact Atoms control how the results are displayed and/or written out: The following are only available when the frequency of checking is when OK/Apply clicked:


UCSF Computer Graphics Laboratory / October 2007