what is command line for find clash chimera write to reply log

Find Clashes/Contacts

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

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

During continuous monitoring, such interactions tin can be shown with choice, coloring, and pseudobonds. Discontinuous monitoring additionally allows writing out information and assigning the largest overlap per cantlet every bit an attribute named overlap. Encounter besides: FindHBond, Intersurf, Rotamers, RR Distance Maps, Crystal Contacts

There are several ways to start Find Clashes/Contacts, a tool in the Structure Assay and Surface/Bounden 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:

• themselves - interactions amongst the designated atoms
• all other atoms (default) - interactions between the designated atoms and all other atoms
• other atoms in same model - intra-model interactions between the designated atoms and all other atoms
• second set of designated atoms - interactions between the designated atoms and a second designated set (specified by selecting atoms and clicking Designate selection as second fix)

Interactions between atoms in different submodels of the same model are ignored (note the findclash command has an option to include such interactions, however). Irresolute the selection will non automatically alter any designated sets.

The Disharmonism/Contact Parameters command what volition be considered a clash or contact. The overlap between 2 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 – assart_ij

• Find atoms with VDW overlap >=[ cutoff ] angstroms - pairs of atoms with overlap ≥ cutoff will be identified. A larger positive cutoff restricts the results to more astringent clashes, whereas a negative cutoff can also identify favorable contacts.
• Subtract [ allowance ] from overlap for potentially H-bonding pairs - an allowance > 0 reflects the observation that atoms sharing a hydrogen bail tin come closer to each other than would be expected from their VDW radii. The allowance is merely 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)). Equally 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 lonely pair.

  For detecting clashes , cutoff values of 0.iv-ane.0 Å and allowance values of 0.2-0.6 Å are generally reasonable (default disharmonism criteria 0.half-dozen and 0.iv Å, respectively).

  For detecting contacts , negative cutoff values of 0.0-(–ane.0) Å with an allowance of 0.0 Å are generally reasonable (default contact criteria –0.4 and 0.0 Å, respectively).

• Ignore contacts of pairs [ North ] or fewer bonds autonomously (Northward=4 by default)
• Include intra-residual contacts (default off)
• Include intra-molecule contacts (default on) - whether to include intramolecular interactions, where a molecule is defined equally a covalently bonded set of atoms

Options for the Handling of Disharmonism/Contact Atoms:

• Select - whether to select atoms meeting the disharmonism/contact criteria (and deselect all other atoms)
• Colour [ color well ] (and color all other atoms [ color well ]) - whether to color atoms meeting and not coming together 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 yellowish) and linewidth (default 2.0) betwixt pairs meeting the clash/contact criteria. These pseudobonds tin can exist removed with the control ~findclash. The PseudoBond Console can also exist used to shut the pseudobond grouping (named contacts) or alter its display.
• If endpoint cantlet hidden, show endpoint residue - turn on the display of residues containing a contact atom if that cantlet is non displayed initially (By default, if the cantlet on either terminate 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.)

  The post-obit are only available for discontinuous checking (when OK/Apply clicked):

• Assign 'overlap' aspect - whether to assign the largest overlap per atom equally an attribute named overlap and open the Render by Attribute tool
• Write data to file - whether to write disharmonism/contact information to a text file. The dialog for saving the file includes a Naming style option to control how atoms volition be listed:
  • simple (for case, HIS xvi.A ND1)
  • command-line specifier (for case, :16.A@ND1)
  • serial number (for example, 126)
• Write information to reply log - whether to write clash/contact information to the Reply Log. The Atomspec display fashion setting in the Labels preferences controls how atoms will be listed.

Options for the Frequency of Checking:

• when OK/Apply clicked (default) - this pick is compatible with all handling options, including attribute assignment and writing out clash/contact information. Clicking OK runs the calculation and dismisses the dialog, whereas clicking Utilize runs the adding without dismissing the dialog.
• subsequently relative motions (until dialog closed) - whenever relative motions are paused; only selection and display treatments are bachelor. Relative motions include bond rotations and translations/rotations of 1 model relative to another, as opposed to translations/rotations of all models collectively.
• continuously (until dialog closed) - during motions; only pick and brandish treatments are available

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UCSF Computer Graphics Laboratory / September 2014

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Source: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html