r14890 - /1.3/test_suite/shared_data/frame_order/rigid/tensor_fit.py -- October 24, 2011 - 00:29

Author: bugman
Date: Mon Oct 24 00:29:08 2011
New Revision: 14890

URL: http://svn.gna.org/viewcvs/relax?rev=14890&view=rev
Log:
Updated the alignment tensor fitting script.


Modified:
    1.3/test_suite/shared_data/frame_order/rigid/tensor_fit.py

Modified: 1.3/test_suite/shared_data/frame_order/rigid/tensor_fit.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/frame_order/rigid/tensor_fit.py?rev=14890&r1=14889&r2=14890&view=diff
==============================================================================
--- 1.3/test_suite/shared_data/frame_order/rigid/tensor_fit.py (original)
+++ 1.3/test_suite/shared_data/frame_order/rigid/tensor_fit.py Mon Oct 24 
00:29:08 2011
@@ -1,37 +1,52 @@
 # Script for calculating the RDC alignment tensors for the test model.
 
+from string import upper
 
-# Create a new data pipe.
-pipe.create('fit', 'N-state')
 
-# Load the rotated C-domain.
-structure.read_pdb('1J7P_1st_NH_rot.pdb', dir='..')
-
-# 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")
+# The tensor file for reading into relax.
+out = open('tensors.py', 'w')
 
 # Loop over the alignments.
-for tag in ['Ln1', 'Ln2', 'Ln3', 'Ln4']:
+ln = ['dy', 'tb', 'tm', 'er']
+for i in range(len(ln)):
+    # Create a new data pipe.
+    pipe.create(ln[i], 'N-state')
+
+    # Load the rotated C-domain.
+    structure.read_pdb('1J7P_1st_NH_rot.pdb', dir='..')
+
+    # 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")
+
     # Load the RDCs.
-    rdc.read(align_id=tag, file='rdc_%s.txt'%tag, spin_id_col=1, data_col=2, 
error_col=None)
+    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)
 
     # Set up the model.
     n_state_model.select_model(model='fixed')
 
     # Minimisation.
-    grid_search(inc=11)
-    minimise('bfgs', constraints=True)
+    grid_search(inc=7)
+    minimise('newton', constraints=True)
 
-    # Fix the tensor.
-    align_tensor.fix(tag)
+    # Monte Carlo simulations.
+    monte_carlo.setup(number=1000)
+    monte_carlo.create_data()
+    monte_carlo.initial_values()
+    minimise('newton', constraints=False)
+    monte_carlo.error_analysis()
 
+    # Alias the tensor.
+    A = cdp.align_tensors[i]
 
+    # Write out the tensors.
+    out.write("align_tensor.init(tensor='%s%s %s-dom', params=(%s, %s, %s, 
%s, %s), param_types=2)\n" % (upper(ln[i][0]), ln[i][1], 'C', A.Axx, A.Ayy, 
A.Axy, A.Axz, A.Ayz))
+    out.write("align_tensor.init(tensor='%s%s %s-dom', params=(%s, %s, %s, 
%s, %s), param_types=2, errors=True)\n" % (upper(ln[i][0]), ln[i][1], 'C', 
A.Axx_err, A.Ayy_err, A.Axy_err, A.Axz_err, A.Ayz_err))