Author: bugman
Date: Tue Dec 13 22:45:52 2011
New Revision: 15090
URL: http://svn.gna.org/viewcvs/relax?rev=15090&view=rev
Log:
Updated the 2nd isotropic cone, free rotor frame order test model
optimisation script.
Modified:
branches/frame_order_testing/test_suite/shared_data/frame_order/iso_cone_free_rotor2/frame_order.py
Modified:
branches/frame_order_testing/test_suite/shared_data/frame_order/iso_cone_free_rotor2/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/frame_order/iso_cone_free_rotor2/frame_order.py?rev=15090&r1=15089&r2=15090&view=diff
==============================================================================
---
branches/frame_order_testing/test_suite/shared_data/frame_order/iso_cone_free_rotor2/frame_order.py
(original)
+++
branches/frame_order_testing/test_suite/shared_data/frame_order/iso_cone_free_rotor2/frame_order.py
Tue Dec 13 22:45:52 2011
@@ -15,27 +15,14 @@
# Optimise.
self.optimisation()
- # The rotation matrix.
- R = zeros((3, 3), float64)
- ave_pos_alpha = 0.0
- if hasattr(cdp, 'ave_pos_alpha') and cdp.ave_pos_alpha != None:
- ave_pos_alpha = cdp.ave_pos_alpha
- euler_to_R_zyz(ave_pos_alpha, cdp.ave_pos_beta, cdp.ave_pos_gamma, R)
- print("Rotation matrix:\n%s\n" % R)
- R = transpose(R)
- print("Inverted rotation:\n%s\n" % R)
-
- # The pivot point.
- pivot = array([ 37.254, 0.5, 16.7465])
-
# Load the original structure.
self.original_structure()
# Domain transformation.
- self.transform(R, pivot)
+ self.transform()
# Display in pymol.
- self.pymol_display(pivot)
+ self.pymol_display()
# Save the state.
state.save('frame_order', force=True)
@@ -44,23 +31,57 @@
def optimisation(self):
"""Optimise the frame order model."""
- # The file paths.
- PATH_N_DOM = '..' + sep
- PATH_C_DOM = '.' + sep
-
# Create the data pipe.
pipe.create(pipe_name='frame order', pipe_type='frame order')
- # Load the tensors.
- script(PATH_N_DOM + 'tensors.py')
- script(PATH_C_DOM + 'tensors.py')
+ # Read the structures.
+ structure.read_pdb('1J7O_1st_NH.pdb', dir='..', set_mol_name='N-dom')
+ structure.read_pdb('1J7P_1st_NH_rot.pdb', dir='..',
set_mol_name='C-dom')
+
+ # Load the spins.
+ structure.load_spins('@N')
+ structure.load_spins('@H')
+
+ # Load the NH vectors.
+ structure.vectors(spin_id='@N', attached='H', ave=False)
+
+ # Set the values needed to calculate the dipolar constant.
+ value.set(1.041 * 1e-10, 'bond_length', spin_id="@N")
+ value.set('15N', 'heteronucleus', spin_id="@N")
+ value.set('1H', 'proton', spin_id="@N")
+
+ # Loop over the alignments.
+ ln = ['dy', 'tb', 'tm', 'er']
+ for i in range(len(ln)):
+ # Load the RDCs.
+ rdc.read(align_id=ln[i], file='rdc_%s.txt'%ln[i], res_num_col=2,
spin_name_col=5, data_col=6, error_col=7)
+
+ # The PCS.
+ pcs.read(align_id=ln[i], file='pcs_%s.txt'%ln[i], res_num_col=2,
spin_name_col=5, data_col=6, error_col=7)
+
+ # The temperature and field strength.
+ temperature(id=ln[i], temp=303)
+ frq.set(id=ln[i], frq=900e6)
+
+ # Load the N-domain tensors (the full tensors).
+ script('../tensors.py')
+
+ # Define the domains.
+ domain(id='N', spin_id=":1-78")
+ domain(id='C', spin_id=":80-144")
# The tensor domains and reductions.
full = ['Dy N-dom', 'Tb N-dom', 'Tm N-dom', 'Er N-dom']
red = ['Dy C-dom', 'Tb C-dom', 'Tm C-dom', 'Er C-dom']
for i in range(len(full)):
+ # Initalise the reduced tensor.
+ align_tensor.init(tensor=red[i], params=(0,0,0,0,0))
+
+ # Set the domain info.
align_tensor.set_domain(tensor=full[i], domain='N')
align_tensor.set_domain(tensor=red[i], domain='C')
+
+ # Specify which tensor is reduced.
align_tensor.reduction(full_tensor=full[i], red_tensor=red[i])
# Select the model.
@@ -69,12 +90,28 @@
# Set the reference domain.
frame_order.ref_domain('N')
+ # Set the initial pivot point.
+ pivot = array([ 37.254, 0.5, 16.7465])
+ frame_order.pivot(pivot, fix=True)
+
+ # Set the paramagnetic centre.
+ paramag.centre(pos=[35.934, 12.194, -4.206])
+
+ # Check the minimum.
+ cdp.ave_pos_beta = 1.1321377968123119
+ cdp.ave_pos_gamma = 0.029867114268410672
+ cdp.axis_theta = -0.70177072973807042
+ cdp.axis_phi = 0.89129130027034131
+ cdp.cone_s1 = 0.9121076263414718
+ calc()
+ print cdp.chi2
+
# Optimise.
- grid_search(inc=3)
+ #grid_search(inc=5)
minimise('simplex', constraints=False)
# Test Monte Carlo simulations.
- monte_carlo.setup(number=500)
+ monte_carlo.setup(number=5)
monte_carlo.create_data()
monte_carlo.initial_values()
minimise('simplex', constraints=False)
@@ -89,10 +126,10 @@
pipe.create(pipe_name='orig pos', pipe_type='frame order')
# Load the structure.
- structure.read_pdb('1J7P_1st_NH.pdb', dir='..')
+ structure.read_pdb('1J7P_1st_NH_rot.pdb', dir='..')
- def pymol_display(self, pivot):
+ def pymol_display(self):
"""Display the results in PyMOL."""
# Switch back to the main data pipe.
@@ -101,9 +138,6 @@
# Load the PDBs of the 2 domains.
structure.read_pdb('1J7O_1st_NH.pdb', dir='..')
structure.read_pdb('1J7P_1st_NH_rot.pdb', dir='..')
-
- # Set the pivot point.
- frame_order.pivot(pivot)
# Create the cone PDB file.
frame_order.cone_pdb(file='cone.pdb', force=True)
@@ -118,8 +152,19 @@
pymol.cone_pdb('cone.pdb')
- def transform(self, R, pivot):
+ def transform(self):
"""Transform the domain to the average position."""
+
+ # Switch back to the main data pipe.
+ pipe.switch('frame order')
+
+ # The rotation matrix.
+ R = zeros((3, 3), float64)
+ euler_to_R_zyz(0.0, cdp.ave_pos_beta, cdp.ave_pos_gamma, R)
+ print("Rotation matrix:\n%s\n" % R)
+ R = transpose(R)
+ print("Inverted rotation:\n%s\n" % R)
+ pivot = cdp.pivot
# Create a special data pipe for the average rigid body position.
pipe.create(pipe_name='ave pos', pipe_type='frame order')
r15090 - /branches/frame_order_testing/test_suite/shared_data/frame_order/iso_cone_free_rotor2/frame_order.py