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',