The clashes and contacts commands are the same except for their default interaction criteria, meant to identify:
A non-blank atom-spec1 is required. The test option indicates whether to look for interactions among the specified atoms or between them and other atoms (details...).
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 – dij – allowanceij
command overlapCutoff (Å) hbondAllowance (Å) default usual range default usual range clashes 0.6 0.4-1.0 0.4 0.2-0.6 contacts −0.4 0.0-(−1.0) 0.0 0.0
Normally, a clash or contact is identified based on the overlap cutoff, but the distanceOnly option allows using a center-to-center distance cutoff instead. Both measures are reported in the detailed results.
By default, clashes/contacts are shown as pseudobonds. A pseudobond is only shown when both of its endpoint atoms are shown; reveal true can be used to display atoms as needed so that all of the interactions will be shown (details...). The pseudobonds can be labeled by distance, and their color, radius, and number of dashes can be specified. The default name of the pseudobond model for creation (and for removal with ~clashes or ~contacts) is clashes or contacts. When multiple pseudobond models have the same name, specific models can be removed with the close command.
During continuous monitoring, such interactions can also be shown with selection and atom coloring. Discontinuous monitoring additionally allows logging the detailed results and/or saving them to a file. The command ~clashes or ~contacts removes the indicated pseudobonds and halts any continuous monitoring.
Pseudobonds can be labeled by length with the label command and changed between solid and dashed with style. An interactive histogram of pseudobond lengths can be plotted with crosslinks histogram, and a chain network diagram summarizing intra- and interchain pseudobonds can be shown with crosslinks network.
test self | others | atom-spec2
Which interactions to find: among atom-spec1 (self), between atom-spec1 and all other atoms (others, default), or between atom-spec1 and atom-spec2. If set to others but there are no other atoms (because atom-spec1 contains all atoms), self is automatically used instead.
Pairs of atoms with overlap ≥ cutoff will be identified. A larger positive cutoff restricts the results to more severe clashes, whereas a negative cutoff can also identify favorable contacts. (default 0.6 Å for clashes and –0.4 Å for contacts; see above for suggested value ranges).
An allowance > 0 reflects the observation that atoms sharing a hydrogen bond can favorably approach each other more closely than would be expected from their VDW radii (default 0.4 Å for clashes and 0.0 Å for contacts; see above for suggested value ranges). In the calculation of overlap, 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)). 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.
Specifying this option indicates ignoring overlap and using center-to-center distance ≤ dist as the interaction criterion instead.
makePseudobonds true | false
Whether to create pseudobonds to show contacts/clashes. Pseudobonds are only displayed when both endpoint atoms are displayed, but the reveal option can be used to ensure showing all of the identified interactions.
reveal true | false
Whether to display all clash/contact atoms to ensure displaying the pseudobonds between them. (Hiding an atom also hides its bonds and pseudobonds.) To avoid showing disconnected atoms, the entire residue will be shown, except that amino acid and nucleic acid residues are split into sidechain and backbone moieties separately displayed by this option. Note that displayed backbone atoms may still be invisible when cartoon is also shown. Floating pseudobonds in the presence of cartoon can be hidden with the command cartoon suppress false, with the side effect of showing any backbone atoms that are displayed but suppressed by the cartoon.
showDist true | false
Whether to label the pseudobonds with the corresponding distances. Label color, size, and font can be adjusted with the label command, which can also be used to add the labels later or to delete them. The distances (pseudobond lengths) can also be plotted as a histogram with crosslinks histogram.
Color to use for the pseudobonds when makePseudobonds is true (default yellow); can be changed later with color.
Radius in Å to use for the pseudobonds (default 0.075); can be changed later with size.
Number of dashes to use for pseudobonds depicting interactions (default 6). Only whole numbers are accepted, with 0 indicating solid sticks. Currently, odd numbers are rounded down to give an even number of dashes. The number of dashes can be changed later with style.
Name for the pseudobond model created to show interactions (default clashes or contacts, also the default name for deletion with ~clashes or ~contacts). Using a new name creates a separate model that can be hidden/shown/closed independently. Names containing spaces must be enclosed in quotation marks.
interModel true | false
Whether to look for interactions between models.
interSubmodel true | false
Whether to look for interactions between submodels of the same model.
Interactions between atoms that are ≤ N bonds apart will be ignored (N=4 by default).
If given, only consider interactions between residues at least N apart in sequence.
intraRes true | false
Whether to include intraresidue interactions.
intraMol true | false
Whether to include intramolecular interactions, where a molecule is defined as a covalently bonded set of atoms.
continuous true | false
Whether to initiate continuous checking, which will continue until the specified atoms are removed, or ~clashes (~contacts) is used, or clashes (contacts) is used again without setting this option to true (since false is the default). Only moving a model relative to another will trigger a new check.
select true | false
Whether to select the identified clash/contact atoms (and deselect all other atoms).
colorAtoms true | false
Whether to color the identified clash/contact atoms the atomColor and the remaining atoms the otherAtomColor.
Color to use for the identified clash/contact atoms when colorAtoms is true (default red).
Color to use for atoms other than the identified clash/contact atoms when colorAtoms is true (default none).
setAttrs true | false
Whether to assign the largest overlap per atom as an attribute. Disallowed with continuous monitoring.
Name for atom attribute (default overlap) assigned when setAttrs is true.
Specify writing contact/clash information to a file (disallowed with continuous monitoring). The information includes atom specifications (see namingStyle), overlaps, and interatomic distances. File is the output file pathname, enclosed in quotation marks if it includes spaces, or the word browse to specify it interactively in a file browser window.
log true | false
Whether to write information (as described above for saveFile) to the Log. Disallowed with continuous monitoring.
namingStyle simple | command | serial
How to describe atoms in contact/clash information written to a file or the log:
Model number will be included when multiple models are present.
- simple (default) - chain ID (preceded by slash), residue name, residue number, atom name (for example, /B ASN 21 OD1)
- command - command-line specifier (for example, /B:21@OD1)
- serial - atom serial number (for example, 126)
summary true | false
Whether to write the total number of interactions found to the status line and Log. During continuous monitoring with summary true, summaries are continually sent to the status line, but only the initial and final summaries are reported in the Log.