Author: bugman
Date: Fri Jul 11 15:38:59 2014
New Revision: 24524
URL: http://svn.gna.org/viewcvs/relax?rev=24524&view=rev
Log:
Added a script for testing out the parameter nesting abilities of the frame
order auto-analysis.
This script attempts to find the dynamics solution without knowing where the
pivot is located.
Hence this will be as in the auto-analysis were this pivot point will be used
as the base for all
other models.
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor/frame_order_free_start.py
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor/frame_order_free_start.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor/frame_order_free_start.py?rev=24524&view=auto
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor/frame_order_free_start.py
(added)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor/frame_order_free_start.py
Fri Jul 11 15:38:59 2014
@@ -0,0 +1,109 @@
+# Script for optimising the rotor frame order test model of CaM.
+
+
+# The real parameter values.
+AVE_POS_X, AVE_POS_Y, AVE_POS_Z = [ -21.269217407269576,
-3.122610661328414, -2.400652421655998]
+AVE_POS_ALPHA, AVE_POS_BETA, AVE_POS_GAMMA = [5.623469076122531,
0.435439405668396, 5.081265529106499]
+
+# Create the data pipe.
+pipe.create(pipe_name='frame order', pipe_type='frame order')
+
+# 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')
+
+# Set up the 15N and 1H spins.
+structure.load_spins(spin_id='@N', ave_pos=False)
+structure.load_spins(spin_id='@H', ave_pos=False)
+spin.isotope(isotope='15N', spin_id='@N')
+spin.isotope(isotope='1H', spin_id='@H')
+
+# Define the magnetic dipole-dipole relaxation interaction.
+interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
+interatom.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.041 * 1e-10)
+interatom.unit_vectors()
+
+# 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], spin_id1_col=1,
spin_id2_col=2, data_col=3, error_col=4)
+
+ # The PCS.
+ pcs.read(align_id=ln[i], file='pcs_%s.txt'%ln[i], mol_name_col=1,
res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
+
+ # The temperature and field strength.
+ spectrometer.temperature(id=ln[i], temp=303)
+ spectrometer.frequency(id=ln[i], frq=900e6)
+
+# Load the N-domain tensors (the full tensors).
+script('../tensors.py')
+
+# Define the domains.
+domain(id='N', spin_id="#N-dom")
+domain(id='C', spin_id="#C-dom")
+
+# 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']
+ids = ['dy', 'tb', 'tm', 'er']
+for i in range(len(full)):
+ # Initialise the reduced tensor.
+ align_tensor.init(tensor=red[i], align_id=ids[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.
+frame_order.select_model('rotor')
+
+# Set the reference domain.
+frame_order.ref_domain('N')
+
+# Set the paramagnetic centre.
+paramag.centre(pos=[35.934, 12.194, -4.206])
+
+# Set the average domain position parameters.
+value.set(param='ave_pos_x', val=AVE_POS_X)
+value.set(param='ave_pos_y', val=AVE_POS_Y)
+value.set(param='ave_pos_z', val=AVE_POS_Z)
+value.set(param='ave_pos_alpha', val=AVE_POS_ALPHA)
+value.set(param='ave_pos_beta', val=AVE_POS_BETA)
+value.set(param='ave_pos_gamma', val=AVE_POS_GAMMA)
+
+# Free the pivot, and set it to the CoM of both domains which is far enough
away from the real pivot.
+frame_order.pivot([ 34.721619683345111, -2.63891199102997 ,
12.941974078087899], fix=False)
+
+# Grid search (low quality for speed).
+frame_order.num_int_pts(num=100)
+grid_search(inc=[11, 11, 11, None, None, None, None, None, None, 11, 11])
+
+# Iterative optimisation with increasing precision.
+num_int_pts = [1000, 10000, 50000]
+func_tol = [1e-2, 1e-3, 1e-4]
+for i in range(len(num_int_pts)):
+ frame_order.num_int_pts(num=num_int_pts[i])
+ minimise('simplex', func_tol=func_tol[i])
+
+# Test Monte Carlo simulations (at low quality for speed).
+frame_order.num_int_pts(num=100)
+monte_carlo.setup(number=5)
+monte_carlo.create_data()
+monte_carlo.initial_values()
+minimise('simplex', func_tol=1e-2)
+eliminate()
+monte_carlo.error_analysis()
+
+# Create the PDB representation.
+frame_order.pdb_model(ave_pos='ave_pos_free_start',
rep='frame_order_free_start', dist=None, compress_type=2, force=True)
+
+# Compare to the true result in PyMOL.
+pymol.frame_order(ave_pos='ave_pos_true', rep='frame_order_true', dist=None)
+pymol.frame_order(ave_pos='ave_pos_free_start',
rep='frame_order_free_start', dist=None)
+
+# Save the state.
+state.save('frame_order_free_start', force=True)
r24524 - /branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor/frame_order_free_start.py