Problem solved, I just needed to attach protons to the X-ray structure. BW Stacia ________________________________________ From: relax-users [relax-users-boun...@gna.org] on behalf of relax-users-requ...@gna.org [relax-users-requ...@gna.org] Sent: 30 January 2017 11:00 To: relax-users@gna.org Subject: relax-users Digest, Vol 119, Issue 3
Send relax-users mailing list submissions to relax-users@gna.org To subscribe or unsubscribe via the World Wide Web, visit https://mail.gna.org/listinfo/relax-users or, via email, send a message with subject or body 'help' to relax-users-requ...@gna.org You can reach the person managing the list at relax-users-ow...@gna.org When replying, please edit your Subject line so it is more specific than "Re: Contents of relax-users digest..." Today's Topics: 1. RelaxError: Positional information could not be found for any spins. (Stanislava Panova) ---------------------------------------------------------------------- Message: 1 Date: Mon, 30 Jan 2017 10:14:01 +0000 From: Stanislava Panova <stanislava.pan...@postgrad.manchester.ac.uk> To: "relax-users@gna.org" <relax-users@gna.org> Subject: RelaxError: Positional information could not be found for any spins. Message-ID: <aa9a9060f9bc3c40832adcb433d5a6b7015fbd0...@mbxp09.ds.man.ac.uk> Content-Type: text/plain; charset="iso-8859-1" Dear all Relax (3.3.0 and 4.0.3) both give me the same error when I try to run dauvergne protocol with local tm setting and structure loaded in: RelaxError: Positional information could not be found for any spins I cannot figure what is wrong. Problem appears at: interatom.unit_vectors() Here is the script contents: # Python module imports. from time import asctime, localtime # relax module imports. from auto_analyses.dauvergne_protocol import dAuvergne_protocol # 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) # Set up the 15N spins. #sequence.read(file='hnoe_800.txt', res_num_col=2, res_name_col=3) #spin.name('N') #spin.element('N') #spin.isotope('15N', spin_id='@N') # Load a PDB file. structure.read_pdb('2xe6.pdb', set_mol_name='PGK', alt_loc='A') 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*') # 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_800', ri_type='R1', frq=800.31*1e6, file='R1_800', 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_800', ri_type='R2', frq=800.31*1e6, file='R2_800', 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_800', ri_type='NOE', frq=800.31*1e6, file='hnoe_800', 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_600', ri_type='R1', frq=599.9*1e6, file='R1_600', 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=599.9*1e6, file='R2_600', 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=599.9*1e6, file='hnoe_600', 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=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. 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) ------------------------------ Subject: Digest Footer _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users ------------------------------ End of relax-users Digest, Vol 119, Issue 3 ******************************************* _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users