Page created by Vikram K. Mulligan (vmulligan@flatironinstitute.org). Last modified 12 October 2018. Back to Mover page.
Crick params files are ASCII files with extension .crick_params. They define the minor helical parameters of polymer helices, such as alpha-helices, 3-10 helices, polyproline type I and II helices, etc. Since strands represent a special case of a helix, in which the turn per residue is about 180 degrees, Crick params files can also define minor helical parameters for a strand. The minor helix parameters are used, along with user-specified major helix parameters, to generate coiled-coil geometry using the Crick equations (first described by Francis Crick in 1953 -- see Crick F. (1953) "The Fourier transform of a coiled-coil". Acta Cryst. 6:685-689).
Crick params files are located in the Rosetta database, in database/protocol_data/crick_parameters/.
Crick params file consist of a series of lines, each specifying either a global property of the helix type or a per-atom parameter value. The allowed entries are:
| Entry | Description | Requirements | Example |
|---|---|---|---|
| Comments | Any line starting with a number sign ("#"). Used to provide information ignored by Rosetta but useful to developers or users. | None, so long as a number sign starts the line. | #Crick params file for a beta-amino acid 14-helix |
| residues_per_repeat | The number of residues in each repeating unit in the minor helix. Defaults to 1 if not specified. | Positive integer. | residues_per_repeat 4 |
| atoms_per_residue | The number of atoms in each residue in the repeating unit. If residues_per_repeat is 1, this is inferred automatically from the number of r1, delta_omega1, and delta_z1 lines. If the number of residues per repeat is greater than 1, this must be specified. | One entry must be included for each residue in the repeating unit, if the repeating unit is more than 1 residue long. The values must be positive integers. | atoms_per_residue 4 |
| omega1 | The twist per residue of the minor helix, in radians per residue. | A single entry must be provided per Crick params file. | omega1 1.30252 |
| z1 | The rise per residue of the minor helix, in Angstroms per residue. | A single entry must be provided per Crick params file. | z1 0.98252 |
| r1 | The per-atom minor helix radius (i.e. the distance of an atom from the minor helix axis). | Must be postive. One entry is required for each atom in the repeating unit. | r1 1.0231515 |
| delta_omega1 | The angular offset about the minor helix axis for each atom, specified in radians, relative to the reference atom. | One entry is required for each atom in the repeating unit. | delta_omega1 0.2352525 |
| delta_z1 | The linear offset along the minor helix axis for each atom, specified in Angstroms, relative to the reference atom. | One entry is required for each atom in the repeating unit. | delta_z1 -0.6352431 |