Re: [bug #20175] run mf_multimodel.py in relax (cmd) -- September 19, 2012 - 17:35

Dear Dr. Edward d  Auvergne,

Attached please find the mf_multimodel.py, which opened and modified  
in a window text file (basic text formatting). By the way, I sent the  
email to relax-devel@xxxxxxx, not to relax-users@xxxxxxx, it is  
correct way ?

Thank you very much.

With best regards,

Mengjun Xue

Quoting Edward d  Auvergne <NO-REPLY.INVALID-ADDRESS@xxxxxxx>:

> Update of bug #20175 (project relax):
>
>                   Status:                    None => Need Info
>              Assigned to:                    None => bugman
>
>     _______________________________________________________
>
> Follow-up Comment #1:
>
> Mengjun, could you attach the script you used as well to this report?  From
> the log file, I can see that there is a formatting problem in your script.
> The bruker.read user functions are all located on the same line whereas they
> should be on separate lines.
>
> This could be a typo, or it could be a problem with the newline formatting
> differences between MS Windows, GNU/Linux and Mac OS X.  Which text editor do
> you use to edit your scripts?
>
>     _______________________________________________________
>
> Reply to this item at:
>
>   <http://gna.org/bugs/?20175>
>
> _______________________________________________
>   Message sent via/by Gna!
>   http://gna.org/


###############################################################################
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# Copyright (C) 2003-2012 Edward d'Auvergne                                   
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# This file is part of the program relax (http://www.nmr-relax.com).          
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#
# This program is free software: you can redistribute it and/or modify        
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# it under the terms of the GNU General Public License as published by        
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# the Free Software Foundation, either version 3 of the License, or           
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# (at your option) any later version.                                         
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# This program is distributed in the hope that it will be useful,             
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# but WITHOUT ANY WARRANTY; without even the implied warranty of              
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               
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# GNU General Public License for more details.                                
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# You should have received a copy of the GNU General Public License           
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# along with this program.  If not, see <http://www.gnu.org/licenses/>.       
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#                                                                             
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###############################################################################

"""This script performs a model-free analysis for the models 'm0' to 'm9' (or 
'tm0' to 'tm9')."""


# Set the data pipe names (also the names of preset model-free models).
#pipes = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 
'tm9']
pipes = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']

# Loop over the pipes.
for name in pipes:
    # Create the data pipe.
    pipe.create(name, 'mf')

    # Set up the 15N spins.
    sequence.read('noe.500.out', res_num_col=1)
    spin.name('N')
    spin.element(element='N', spin_id='@N')
    spin.isotope('15N', spin_id='@N')

    # Load a PDB file.
    structure.read_pdb(file='C:\\Documents and Settings\\Mengjun 
Xue\\Desktop\\Relax bugs\\Relax\\tutorial_pdc\\tutorial_pdc\\1UBQ_H.pdb', 
dir=None, read_mol=None, set_mol_name=None, read_model=None, 
set_model_num=None, parser='internal')

    # Load the relaxation data.
    bruker.read(ri_id='noe_600', file='C:\\Documents and Settings\\Mengjun 
Xue\\Desktop\\Relax bugs\\Relax\\NOE demo.txt', dir=None)   
bruker.read(ri_id='r1_600', file='C:\\Documents and Settings\\Mengjun 
Xue\\Desktop\\Relax bugs\\Relax\\T1 demo.txt', dir=None)   
bruker.read(ri_id='r2_600', file='C:\\Documents and Settings\\Mengjun 
Xue\\Desktop\\Relax bugs\\Relax\\T2 demo.txt', dir=None) # Set up the 
diffusion tensor.
    diffusion_tensor.init(1e-8, fixed=True)
    #diffusion_tensor.init((1e-8, 1.0, 60, 290), param_types=0, 
spheroid_type='oblate', fixed=True)

    # Generate the 1H spins for the magnetic dipole-dipole relaxation 
interaction.
    sequence.attach_protons()

    # 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)
    structure.get_pos('@N')
    structure.get_pos('@H')
    dipole_pair.unit_vectors()

    # Define the chemical shift relaxation interaction.
    value.set(-172 * 1e-6, 'csa', spin_id='@N')

    # Select the model-free model.
    model_free.select_model(model=name)

    # Minimise.
    grid_search(inc=11)
    minimise('newton')

    # Write the results.
    results.write(file='results', force=True)

# Save the program state.
state.save('save', force=True)