r9377 - /1.3/sample_scripts/jw_mapping.py -- August 24, 2009 - 18:12

Author: bugman
Date: Mon Aug 24 18:12:32 2009
New Revision: 9377

URL: http://svn.gna.org/viewcvs/relax?rev=9377&view=rev
Log:
Converted the J(w) mapping sample script to the relax 1.3 design.

The problem of the old 1.2 line code was discovered by Leao Lagarto 
<dodgy_spin att yahoo ddot co
dot uk> in the thread starting at 
https://mail.gna.org/public/relax-devel/2009-08/msg00004.html
(Message-id: <44680.10570.qm@xxxxxxxxxxxxxxxxxxxxxxxxxxx>).


Modified:
    1.3/sample_scripts/jw_mapping.py

Modified: 1.3/sample_scripts/jw_mapping.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/jw_mapping.py?rev=9377&r1=9376&r2=9377&view=diff
==============================================================================
--- 1.3/sample_scripts/jw_mapping.py (original)
+++ 1.3/sample_scripts/jw_mapping.py Mon Aug 24 18:12:32 2009
@@ -1,40 +1,40 @@
 # Script for reduced spectral density mapping.
 
-# Create the run.
-name = 'jw'
-pipe.create(name, 'jw')
-
-# Nuclei type
-value.set('15N', 'heteronucleus')
+# Create the data pipe.
+pipe.create('my_protein', 'jw')
 
 # Load the sequence.
-sequence.read(name, 'noe.600.out')
+sequence.read('noe.600.out')
 
 # Load the relaxation data.
-relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'r1.600.out')
-relax_data.read(name, 'R2', '600', 600.0 * 1e6, 'r2.600.out')
-relax_data.read(name, 'NOE', '600', 600.0 * 1e6, 'noe.600.out')
+relax_data.read('R1', '600', 600.0 * 1e6, 'r1.600.out')
+relax_data.read('R2', '600', 600.0 * 1e6, 'r2.600.out')
+relax_data.read('NOE', '600', 600.0 * 1e6, 'noe.600.out')
+
+# Set the nuclei types.
+value.set('15N', 'heteronucleus')
+value.set('1H', 'proton')
 
 # Set the bond length and CSA values.
-value.set(name, 1.02 * 1e-10, 'bond_length')
-value.set(name, -172 * 1e-6, 'csa')
+value.set(1.02 * 1e-10, 'bond_length')
+value.set(-172 * 1e-6, 'csa')
 
 # Select the frequency.
-jw_mapping.set_frq(name, frq=600.0 * 1e6)
+jw_mapping.set_frq(frq=600.0 * 1e6)
 
 # Reduced spectral density mapping.
-calc(name)
+calc()
 
-# Monte Carlo simulations.
-monte_carlo.setup(name, number=500)
-monte_carlo.create_data(name)
-calc(name)
-monte_carlo.error_analysis(name)
+# Monte Carlo simulations (well, bootstrapping as this is a calculation and 
not a fit!).
+monte_carlo.setup(number=500)
+monte_carlo.create_data()
+calc()
+monte_carlo.error_analysis()
 
 # Create grace files.
-grace.write(name, y_data_type='j0', file='j0.agr', force=True)
-grace.write(name, y_data_type='jwx', file='jwx.agr', force=True)
-grace.write(name, y_data_type='jwh', file='jwh.agr', force=True)
+grace.write(y_data_type='j0', file='j0.agr', force=True)
+grace.write(y_data_type='jwx', file='jwx.agr', force=True)
+grace.write(y_data_type='jwh', file='jwh.agr', force=True)
 
 # View the grace files.
 grace.view(file='j0.agr')