Hello I ran the model free analysis without structure using dauvergne_protocol.py in Relax3.0.0. Like this. # Analysis variables. | ##################### | | # The diffusion model. | DIFF_MODEL = 'local_tm' | | # The model-free models. Do not change these unless absolutely necessary, the protocol is likely to fail if these are changed. | MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9'] | LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 'tm9'] | | # The grid search size (the number of increments per dimension). | GRID_INC = 11 | | # The optimisation technique. | MIN_ALGOR = 'newton' | | # The number of Monte Carlo simulations to be used for error analysis at the end of the analysis. | MC_NUM = 500 | | # Automatic looping over all rounds until convergence (must be a boolean value of True or False). | CONV_LOOP = True | | | | # Set up the data pipe. | ####################### | | # The following sequence of user function calls can be changed as needed. | | # Create the data pipe. | pipe_bundle = "mf (%s)" % asctime(localtime()) | name = "origin - " + pipe_bundle | pipe.create(name, 'mf', bundle=pipe_bundle) | | # Load the PDB file. | #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) | #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='seq.out', dir=None, spin_num_col=1, spin_name_col=2, res_num_col=3, res_name_col=4) | spin.element(element='N', spin_id='@N*') | #spin.element(element='H', spin_id='@H*') | 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='NOE_600', ri_type='NOE', frq=600.133*1e6, file='NOE.600.out', spin_num_col=1, spin_name_col=2, res_num_col=3, res_name_col=4, data_col=5, error_col=6) | relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.133*1e6, file='R1.600.out', spin_num_col=1, spin_name_col=2, res_num_col=3, res_name_col=4, data_col=5, error_col=6) | relax_data.read(ri_id='R2_600', ri_type='R2', frq=600.133*1e6, file='R2.600.out', spin_num_col=1, spin_name_col=2, res_num_col=3, res_name_col=4, data_col=5, error_col=6) | relax_data.read(ri_id='R1_800', ri_type='R1', frq=800.444*1e6, file='R1.800.out', spin_num_col=1, spin_name_col=2, res_num_col=3, res_name_col=4, data_col=5, error_col=6) | relax_data.read(ri_id='R2_800', ri_type='R2', frq=800.444*1e6, file='R2.800.out', spin_num_col=1, spin_name_col=2, res_num_col=3, res_name_col=4, data_col=5, error_col=6) | relax_data.read(ri_id='NOE_800', ri_type='NOE', frq=800.444*1e6, file='NOE.800.out', spin_num_col=1, spin_name_col=2, res_num_col=3, res_name_col=4, data_col=5, error_col=6) | | #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=3, res_name_col=4, spin_num_col=1, spin_name_col=2, 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. | interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True) | #interatom.define(spin_id1='@NE1', spin_id2='@HE1', direct_bond=True) | interatom.set_dist(spin_id1='@N*', spin_id2='@H*', ave_dist=1.02 * 1e-10) | interatom.unit_vectors() | | # Define the chemical shift relaxation interaction. | value.set(-172 * 1e-6, 'csa', spin_id='@N*') | | | | # Execution. | ############ | | # Do not change! | dAuvergne_protocol(pipe_name=name, pipe_bundle=pipe_bundle, diff_model=DIFF_MODEL, mf_models=MF_MODELS, local_tm_models=LOCAL_TM_MODELS, grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_sim_num=MC_NUM, conv_loop=CONV_LOOP) However, I fail to run this program. This program stopped with this message “relax> interatom.unit_vector(ave=true) Averaging all vectors. RelaxError: positional information could not be found for any spins.” How I can solve this problem. Thank You |
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Kim, Ji Hun Rm. 5110A MRBIII, 465 21st Ave S. Vanderbilt University School of Medicine, Nashville, TN 37232-8725 Phone: 615-936-3757 / Fax: 615-936-2211
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model free analysis without structure