Select and set up the Frame Order model.
model: The name of the preset Frame Order model.
Prior to optimisation, the Frame Order model should be selected. These models consist of three parameter categories:
- The average domain position. This includes the parameters ave_pos_alpha, ave_pos_beta, and ave_pos_gamma. These Euler angles rotate the tensors from the arbitrary PDB frame of the moving domain to the average domain position.
- The frame order eigenframe. This includes the parameters eigen_alpha, eigen_beta, and eigen_gamma. These Euler angles define the major modes of motion. The cone central axis is defined as the z-axis. The pseudo-elliptic cone x and y-axes are defined as the x and y-axes of the eigenframe.
- The cone parameters. These are defined as the tilt-torsion angles cone_theta_x, cone_theta_y, and cone_sigma_max. The cone_theta_x and cone_theta_y parameters define the two cone opening angles of the pseudo-ellipse. The amount of domain torsion is defined as the average domain position, plus and minus cone_sigma_max. The isotropic cones are defined by setting cone_theta_x = cone_theta_y and converting the single parameter into a 2
nd rank order parameter.
The list of available models are:
- `pseudo-ellipse' -
- The pseudo-elliptic cone model. This is the full model consisting of the parameters ave_pos_alpha, ave_pos_beta, ave_pos_gamma, eigen_alpha, eigen_beta, eigen_gamma, cone_theta_x, cone_theta_y, and cone_sigma_max.
- `pseudo-ellipse, torsionless' -
- The pseudo-elliptic cone with the torsion angle cone_sigma_max set to zero.
- `pseudo-ellipse, free rotor' -
- The pseudo-elliptic cone with no torsion angle restriction.
- `iso cone' -
- The isotropic cone model. The cone is defined by a single order parameter s1 which is related to the single cone opening angle cone_theta_x = cone_theta_y. Due to rotational symmetry about the cone axis, the average position α Euler angle ave_pos_alpha is dropped from the model. The symmetry also collapses the eigenframe to a single z-axis defined by the parameters axis_theta and axis_phi.
- `iso cone, torsionless' -
- The isotropic cone model with the torsion angle cone_sigma_max set to zero.
- `iso cone, free rotor' -
- The isotropic cone model with no torsion angle restriction.
- `rotor' -
- The only motion is a rotation about the cone axis restricted by the torsion angle cone_sigma_max.
- `rigid' -
- No domain motions.
- `free rotor' -
- The only motion is free rotation about the cone axis.
- `double rotor' -
- Restricted motions about two independent but orthogonal rotor axes. The first rotation is about the y-axis and the second is about the x-axis.
To select the isotropic cone model, type:
relax> frame_order.select_model(model='iso cone')
The relax user manual (PDF), created 2016-10-28.