Find Clashes/Contacts

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.

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:

overlap_ij = r_VDWi + r_VDWj – d_ij – allowance_ij

Find atoms with VDW overlap >=[ cutoff ] angstroms - pairs of atoms with overlap ≥ cutoff (default 0.6 Å) will be identified. A larger positive cutoff restricts the results to more severe clashes, whereas a negative cutoff can be used to identify favorable contacts.
Subtract [ allowance ] from overlap for potentially H-bonding pairs - an allowance > 0 (default 0.4 Å) reflects the observation that atoms sharing a hydrogen bond can favorably approach each other more closely than would be expected from their VDW radii. The allowance is only subtracted for pairs comprised of a donor (or donor-borne hydrogen) and an acceptor. This is equivalent to using smaller radii to characterize hydrogen-bonding interactions (for example, see Li and Nussinov, Proteins 32:111 (1998)). As in FindHBond, possible donor groups are hydrogen-bearing nitrogen, oxygen, and sulfur atoms, and possible acceptor groups are nitrogen, oxygen, and sulfur atoms with a lone pair.
Ignore overlaps of pairs [ N ] or fewer bonds apart (N=4 by default)
Ignore intra-residue overlaps (on by default)

For detecting clashes, cutoff values in the range 0.4-1.0 Å and allowance values in the range 0.2-0.6 Å are generally reasonable. For detecting contacts, negative cutoff values of –(0.4-1.0) Å with an allowance of 0.0 Å are generally reasonable. The precise values to use depend on the desired stringency of detection and the quality of the structure(s).

Options for the Frequency of Checking:

when OK/Apply clicked (default) - this option is compatible with all outputs, including attribute assignment and writing out clash/contact information. Clicking OK runs the calculation and dismisses the dialog, whereas clicking Apply runs the calculation without dismissing the dialog.
after any motion (until dialog closed) - whenever motion is paused; only selection and display outputs are available
continuously (until dialog closed) - during motion; only selection and display outputs are available

Settings under Treatment of Clash/Contact Atoms control how the results are displayed and/or written out:

Select - whether to select atoms meeting the clash/contact criteria (and deselect all other atoms)
Color [ color well ] (and color all other atoms [ color well ]) - whether to color atoms meeting and not meeting the clash/contact criteria (the default colors are red and No color, respectively; using No color reveals model-level colors)
Draw pseudobonds of color [ color well ] and width [ linewidth ] - whether to draw pseudobonds of the specified color (default yellow) and linewidth (default 2.0) between pairs meeting the clash/contact criteria

The following are only available when the frequency of checking is when OK/Apply clicked:

Assign 'overlap' attribute - whether to assign the largest overlap per atom as an attribute named overlap and open the Render by Attribute tool
Write information to file - whether to write clash/contact information to a text file. The dialog for saving the file includes a Naming style option to control how atoms will be specified in the file.
Write information to reply log - whether to write clash/contact information to the Reply Log. Atomspec display style in the General preferences controls how atoms will be specified.

UCSF Computer Graphics Laboratory / August 2006