Author: bugman
Date: Tue Aug 3 16:22:39 2010
New Revision: 11392
URL: http://svn.gna.org/viewcvs/relax?rev=11392&view=rev
Log:
The frame_order.select_model() user fn docstring now describes all 12
parametric restriction models.
Modified:
1.3/prompt/frame_order.py
Modified: 1.3/prompt/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/frame_order.py?rev=11392&r1=11391&r2=11392&view=diff
==============================================================================
--- 1.3/prompt/frame_order.py (original)
+++ 1.3/prompt/frame_order.py Tue Aug 3 16:22:39 2010
@@ -178,15 +178,63 @@
Description
~~~~~~~~~~~
- Prior to optimisation, the Frame Order model should be selected.
The list of available
- models are:
-
- 'iso cone' - The isotropic cone model. The cone is defined by a
single opening angle
- theta. The torsion angle sigma is unrestricted.
-
- 'pseudo-ellipse' - The pseudo-elliptic cone model. The cone is
defined by two opening
- angles, theta_x and theta_y. In the tilt-torsion angle system
these define the
- allowable tilt. The torsion angle sigma is restricted.
+ 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 2nd 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
alpha 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.
+
+ 'line' - The line cone model. This is the pseudo-elliptic cone
with one of the cone
+ angles, cone_theta_y, assumed to be statistically negligible.
I.e. the cone angle is
+ so small that it cannot be distinguished from noise.
+
+ 'line, torsionless' - The line cone model with the torsion angle
cone_sigma_max set to
+ zero.
+
+ 'line, free rotor' - The line 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.
Examples
r11392 - /1.3/prompt/frame_order.py