cdp.ave_pos_beta = 2.0
cdp.ave_pos_gamma = 2.14159265359
# Set the pivot parameter.
cdp.pivot_disp = 100.0
# Set the eigenframe parameters to allow the minimise.calculate user function to operate.
cdp.axis_alpha = 1.0
cdp.axis_theta = 1.0
cdp.axis_phi = 1.0
cdp.eigen_alpha = 1.0
cdp.eigen_beta = 1.0
cdp.eigen_gamma = 1.0
# Set the order parameters to insignificant values.
cdp.cone_theta = 0.0
cdp.cone_theta_x = 0.0
cdp.cone_theta_y = 0.0
cdp.cone_sigma_max = 0.0
cdp.cone_sigma_max_2 = 0.0
# Allow for stand-alone operation.
if not hasattr(ds, 'model'):
ds.model = 'rigid'
# Select the Frame Order model.
self._execute_uf(uf_name='frame_order.select_model', model=ds.model)
# Calculate the chi2 value.
self._execute_uf(uf_name='minimise.calculate')
# relax imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from specific_analyses.setup import n_state_model_obj
from status import Status; status = Status()
# Path of the files.
str_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'lactose'
data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'align_data'
# Create the data pipe.
self._execute_uf('lactose', 'N-state', uf_name='pipe.create')
# The population model for free operation of this script.
if not hasattr(ds, 'model'):
ds.model = 'population'
# Load the structures.
NUM_STR = 4
for i in range(NUM_STR):
self._execute_uf(uf_name='structure.read_pdb', file='lactose_MCMM4_S1_'+repr(i+1), dir=str_path, set_model_num=i+1, set_mol_name='lactose_MCMM4_S1')
# Set up the 13C and 1H spins information.
self._execute_uf(uf_name='structure.load_spins', spin_id=':UNK@C*', ave_pos=False)
self._execute_uf(uf_name='structure.load_spins', spin_id=':UNK@H*', ave_pos=False)
self._execute_uf(uf_name='spin.isotope', isotope='13C', spin_id='@C*')
self._execute_uf(uf_name='spin.isotope', isotope='1H', spin_id='@H*')
# Deselect the CH2 protons (the rotation of these doesn't work in the model, but the carbon doesn't move).
self._execute_uf(uf_name='deselect.spin', spin_id=':UNK@H6')
self._execute_uf(uf_name='deselect.spin', spin_id=':UNK@H7')
# Set the paramagnetic centre position.
self._execute_uf(uf_name='paramag.centre', pos=[-5, -7, -9])
# Set the number of integration points.
self._execute_uf(uf_name='frame_order.num_int_pts', num=10000)
# Set the real parameter values (the inverted displacement values).
cdp.ave_pos_x = -1
cdp.ave_pos_y = -2
cdp.ave_pos_z = -3
cdp.ave_pos_alpha = 0.14159265359
cdp.ave_pos_beta = 2.0
cdp.ave_pos_gamma = 2.14159265359
# Set some parameters close to zero, but far enough away from zero to allow for the numerical integration.
cdp.cone_s1 = 0.99
cdp.cone_theta = 0.1
cdp.cone_theta_x = 0.1
cdp.cone_theta_y = 0.1
cdp.cone_sigma_max = 0.1
# Allow for stand-alone operation.
if not hasattr(ds, 'model'):
ds.model = 'rigid'
# Select the Frame Order model.
self._execute_uf(uf_name='frame_order.select_model', model=ds.model)
# Calculate the chi2 value.
self._execute_uf(uf_name='calc')
from data_store import Relax_data_store
ds = Relax_data_store()
from specific_analyses.api import return_api
from status import Status
status = Status()
# Path of the files.
str_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'structures' + sep + 'lactose'
data_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'align_data'
# Create the data pipe.
self._execute_uf('lactose', 'N-state', uf_name='pipe.create')
# The population model for free operation of this script.
if not hasattr(ds, 'model'):
ds.model = 'population'
# Load the structures.
NUM_STR = 4
for i in range(NUM_STR):
self._execute_uf(uf_name='structure.read_pdb',
file='lactose_MCMM4_S1_' + repr(i + 1),
dir=str_path,
set_model_num=i + 1,
set_mol_name='lactose_MCMM4_S1')
# Set up the 13C and 1H spins information.
self._execute_uf(uf_name='structure.load_spins',
spin_id=':UNK@C*',
ave_pos=False)
self._execute_uf(uf_name='structure.load_spins',
