r8771 - /1.3/test_suite/system_tests/scripts/align_fit.py -- February 11, 2009 - 14:15

Author: bugman
Date: Wed Feb 11 14:14:59 2009
New Revision: 8771

URL: http://svn.gna.org/viewcvs/relax?rev=8771&view=rev
Log:
Added a script for testing out the use of RDCs and PCSs to find the alignment 
tensor.


Added:
    1.3/test_suite/system_tests/scripts/align_fit.py

Added: 1.3/test_suite/system_tests/scripts/align_fit.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/align_fit.py?rev=8771&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/scripts/align_fit.py (added)
+++ 1.3/test_suite/system_tests/scripts/align_fit.py Wed Feb 11 14:14:59 2009
@@ -1,0 +1,48 @@
+"""Script for testing the fitting an alignment tensor to RDCs or PCSs."""
+
+# Python module imports.
+import sys
+
+
+# Path of the alignment data and structure.
+DATA_PATH = sys.path[-1] + '/test_suite/shared_data/align_data/CaM'
+STRUCT_PATH = sys.path[-1] + '/test_suite/shared_data/structures'
+
+# Create the data pipe.
+pipe.create('rdc', 'N-state')
+
+# Load the CaM structure.
+structure.read_pdb(file='bax_C_1J7P_N_H_Ca', dir=STRUCT_PATH)
+
+# Load the spins.
+structure.load_spins()
+
+# Load the NH vectors.
+structure.vectors(spin_id='@N', attached='H')
+
+# Set the values needed to calculate the dipolar constant.
+value.set(1.02 * 1e-10, 'bond_length', spin_id="@N")
+value.set('15N', 'heteronucleus', spin_id="@N")
+value.set('1H', 'proton', spin_id="@N")
+
+# Load the RDCs and PCSs.
+rdc.read(id='synth', file='synth_rdc', dir=DATA_PATH, mol_name_col=0, 
res_num_col=1, res_name_col=2, spin_num_col=3, spin_name_col=4, data_col=5, 
error_col=6)
+pcs.read(id='synth', file='synth_pcs', dir=DATA_PATH, mol_name_col=0, 
res_num_col=1, res_name_col=2, spin_num_col=3, spin_name_col=4, data_col=5, 
error_col=6)
+
+# The temperature.
+temperature(id='synth', temp=303)
+
+# The frequency.
+frq.set(id='synth', frq=600.0 * 1e6)
+
+# Set up the model.
+n_state_model.select_model(model='fixed')
+
+# Minimisation.
+minimise('simplex', constraints=False, max_iter=5)
+
+# Write out a results file.
+results.write('results', force=True)
+
+# Show the tensors.
+align_tensor.display()