Usage:
findclash  atom-spec  options

Usage:
~findclash

Findclash identifies interatomic clashes and contacts based on VDW radii and user-specified criteria. It is the command-line implementation of Find Clashes/Contacts. Terminology:

• clashes - unfavorable interactions where atoms are too close together; close contacts
• contacts - all kinds of direct interactions: polar and nonpolar, favorable and unfavorable (including clashes)

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

Option keywords for findclash can be truncated to unique strings and their case does not matter. A vertical bar "|" designates mutually exclusive options, and default values are indicated with bold. Synonyms for true: True, 1. Synonyms for false: False, 0.

test  atom-spec | other | model | self
Which interactions to find: between the specified atoms and a second set of atoms (indicated by atom-spec), between the specified atoms and all other atoms (other or others, default), intra-model interactions between the specified atoms and all other atoms (model), or among the specified atoms (self). If atom-spec includes any spaces, it must be enclosed in single or double quote marks.

interSubmodel true | false
Whether to look for interactions between submodels of the same model.

overlapCutoff cutoff
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 also identify favorable contacts.

• For detecting clashes, a cutoff of 0.4-1.0 Å and a hydrogen bond allowance of 0.2-0.6 Å are recommended. The findclash command defaults are the same as the default clash criteria in the Find Clashes/Contacts graphical interface: 0.6 and 0.4 Å, respectively.
  
  
• For detecting contacts, negative cutoff values of 0.0-(–1.0) Å are recommended along with a hydrogen bond allowance of 0.0 Å. The default contact criteria in the Find Clashes/Contacts graphical interface are –0.4 and 0.0 Å, respectively.

hbondAllowance allowance
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. See above for suggested values. 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)). 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.

bondSeparation N
Interactions between atoms that are ≤ N bonds apart will be ignored (N=4 by default).

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 ~findclash is used, or findclash 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, whereas continuous checking with the Find Clashes/Contacts graphical interface will also detect changes from bond rotation or trajectory playback, regardless of relative model motion.

selectClashes true | false
Whether to select the identified clash/contact atoms (and deselect all other atoms).

colorClashes true | false
Whether to color the identified clash/contact atoms the clashColor and the remaining atoms the nonclashColor.

clashColor colorname
Color to use for the identified clash/contact atoms when colorClashes is true (default red). Colorname can be none or any color name that specifies a single color.

nonclashColor colorname
Color to use for atoms other than the identified clash/contact atoms when colorClashes is true (default none, which removes per-atom color assignments and reveals the model-level colors). Colorname can be none or any color name that specifies a single color.

makePseudobonds true | false
Whether to create pseudobonds to show the identified interactions. These pseudobonds can be removed with the command ~findclash. The PseudoBond Panel can also be used to close the pseudobond group (named contacts) or alter its display.

pbColor colorname
Color to use for the pseudobonds when makePseudobonds is true (default yellow). Colorname can be none or any color name that specifies a single color.

lineWidth width
Line width to use for the pseudobonds when makePseudobonds is true (default 2.0 pixels).

reveal true | false
Whether to turn on the display of residues containing a contact atom if that atom is not displayed initially. (By default, if the atom on either end of a pseudobond representing a contact is not shown, the pseudobond itself is not shown, although it still exists; displaying the atom allows the contact pseudobond to be shown.)

setAttrs true | false
Whether to assign the largest overlap per atom as an attribute named overlap. Disallowed with continuous monitoring.

saveFile file
Whether to write contact/clash information to a file (this option is off unless specified). The information includes atom specifications (see namingStyle), overlaps, and interatomic distances. File is the output file name/pathname; if it includes spaces, it must be enclosed in single or double quote marks. If file is browse or browser, a dialog for saving the file will appear (unless the word is enclosed in quotes, which would generate an output file by that name). Disallowed with continuous monitoring.

log true | false
Whether to write contact/clash information (as described above for saveFile) to the Reply Log. Disallowed with continuous monitoring.

namingStyle simple | command | serial
How to describe atoms in contact/clash information written to a file or the log:

• simple - residue name, residue specifier, and atom name (for example, HIS 16.A ND1)
• command or command-line - command-line specifier (for example, :16.A@ND1)
• serial or serialnumber - atom serial number (for example, 126)

Model number will be included when multiple models are present. If namingStyle is not supplied, the Atomspec display style specified in the Labels preferences will be used.

summary true | false
Whether to write the total number of interactions found to the status line and Reply Log.