Author: bugman
Date: Thu Sep 20 11:41:19 2012
New Revision: 17524
URL: http://svn.gna.org/viewcvs/relax?rev=17524&view=rev
Log:
Modified the dauvergne_protocol sample script to handle tryptophan indole NE1
data.
Modified:
trunk/sample_scripts/model_free/dauvergne_protocol.py
Modified: trunk/sample_scripts/model_free/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/sample_scripts/model_free/dauvergne_protocol.py?rev=17524&r1=17523&r2=17524&view=diff
==============================================================================
--- trunk/sample_scripts/model_free/dauvergne_protocol.py (original)
+++ trunk/sample_scripts/model_free/dauvergne_protocol.py Thu Sep 20 11:41:19
2012
@@ -180,42 +180,43 @@
pipe.create(name, 'mf', bundle=pipe_bundle)
# Load the PDB file.
-structure.read_pdb('1f3y.pdb')
-
-# Set up the 15N and 1H spins.
+structure.read_pdb('1f3y.pdb', set_mol_name='Ap4Aase', read_model=3)
+
+# Set up the 15N and 1H spins (both backbone and Trp indole sidechains).
structure.load_spins('@N', ave_pos=True)
+structure.load_spins('@NE1', ave_pos=True)
structure.load_spins('@H', ave_pos=True)
-spin.isotope('15N', spin_id='@N')
-spin.isotope('1H', spin_id='@H')
+structure.load_spins('@HE1', ave_pos=True)
+spin.isotope('15N', spin_id='@N*')
+spin.isotope('1H', spin_id='@H*')
# Set up the 15N spins (alternative to the structure-based approach).
-#sequence.read(file='noe.500.out', dir=None, mol_name_col=None,
res_num_col=1, res_name_col=2, spin_num_col=None, spin_name_col=None)
-#spin.name('N')
-#spin.element(element='N', spin_id='@N')
-#spin.isotope('15N', spin_id='@N')
+#sequence.read(file='noe.500.out', dir=None, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5)
+#spin.element(element='N', spin_id='@N*')
+#spin.isotope('15N', spin_id='@N*')
# Generate the 1H spins for the magnetic dipole-dipole relaxation
interaction (alternative to the structure-based approach).
#sequence.attach_protons()
# Load the relaxation data.
-relax_data.read(ri_id='R1_600', ri_type='R1', frq=599.719*1e6,
file='r1.600.out', mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
-relax_data.read(ri_id='R2_600', ri_type='R2', frq=599.719*1e6,
file='r2.600.out', mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
-relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=599.719*1e6,
file='noe.600.out', mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
-relax_data.read(ri_id='R1_500', ri_type='R1', frq=500.208*1e6,
file='r1.500.out', mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
-relax_data.read(ri_id='R2_500', ri_type='R2', frq=500.208*1e6,
file='r2.500.out', mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
-relax_data.read(ri_id='NOE_500', ri_type='NOE', frq=500.208*1e6,
file='noe.500.out', mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
+relax_data.read(ri_id='R1_600', ri_type='R1', frq=599.719*1e6,
file='r1.600.out', mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
+relax_data.read(ri_id='R2_600', ri_type='R2', frq=599.719*1e6,
file='r2.600.out', mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
+relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=599.719*1e6,
file='noe.600.out', mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
+relax_data.read(ri_id='R1_500', ri_type='R1', frq=500.208*1e6,
file='r1.500.out', mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
+relax_data.read(ri_id='R2_500', ri_type='R2', frq=500.208*1e6,
file='r2.500.out', mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
+relax_data.read(ri_id='NOE_500', ri_type='NOE', frq=500.208*1e6,
file='noe.500.out', mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
# Deselect spins to be excluded (including unresolved and specifically
excluded spins).
-deselect.read(file='unresolved', dir=None, spin_id_col=None,
mol_name_col=None, res_num_col=1, res_name_col=None, spin_num_col=None,
spin_name_col=None, sep=None, spin_id=None, boolean='AND', change_all=False)
+deselect.read(file='unresolved', dir=None, spin_id_col=None, mol_name_col=1,
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None,
spin_id=None, boolean='AND', change_all=False)
deselect.read(file='exclude', spin_id_col=1)
# Define the magnetic dipole-dipole relaxation interaction.
-dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
-dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02 * 1e-10)
+dipole_pair.define(spin_id1='@N*', spin_id2='@H*', direct_bond=True)
+dipole_pair.set_dist(spin_id1='@N*', spin_id2='@H*', ave_dist=1.02 * 1e-10)
dipole_pair.unit_vectors()
# Define the chemical shift relaxation interaction.
-value.set(-172 * 1e-6, 'csa', spin_id='@N')
+value.set(-172 * 1e-6, 'csa', spin_id='@N*')
r17524 - /trunk/sample_scripts/model_free/dauvergne_protocol.py