Re: model free analysis: spin deselection problem -- November 19, 2015

On 19 November 2015 at 13:03, Alain Oregioni <Alain.Oregioni@xxxxxxxxxxx> 
wrote:

Hi Edward,

Thanks for your reply. I was out of the office till now, so I've not had
time to debug more till now.

 I had a look at the log and I didn't see any warning earlier than the ones
I mentioned, so I'm again stuck. I will check for name mismatch though, as
this has happened before.

Sorry about the attachments, I'm afraid I didn't read the communication
protocols...Here's the beginning of the script:

#################################################################################

# The diffusion model.
DIFF_MODEL = 'prolate'

# 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 = 13

# 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

# The local paths.
SEQ_PATH =
'C:\\Users\\aoregio\\Desk\\Crick\\Projects\\Woolfson_coiledCoil\\RC'


# 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('4DZM-CC-pIL-I17N-dimer-AsnA.pdb', dir='.',
set_mol_name=['CCDi_mol1','CCDi_mol2'], alt_loc='A')

# Set up the 15N and 1H spins (both backbone and Trp indole sidechains).
#structure.load_spins(spin_id='@N', ave_pos=False)
structure.load_spins(spin_id=':6@N', ave_pos=False)
structure.load_spins(spin_id=':13@N', ave_pos=False)
structure.load_spins(spin_id=':17@N', ave_pos=False)
structure.load_spins(spin_id=':20@N', ave_pos=False)
structure.load_spins(spin_id=':27@N', ave_pos=False)

spin.isotope('15N', spin_id='@N*')
spin.isotope('1H', spin_id='@H*')

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


Hi Alain,

The problem is right here!  The sequence.attach_protons user function
is only for use when you don't have a 3D structure
(http://www.nmr-relax.com/manual/sequence_attach_protons.html).  I
should probably document that better!  Ok, done:

    http://article.gmane.org/gmane.science.nmr.relax.scm/25823

You should load your protons from the 3D structure with
structure.load_spins user function calls
(http://www.nmr-relax.com/manual/structure_load_spins.html).  That way
the proton spin containers will have atomic coordinates, and the NH
bond vectors can then be calculated (which you'll need to add to your
script, see http://www.nmr-relax.com/manual/interatom_unit_vectors.html).
For more details, see:

    
http://www.nmr-relax.com/manual/d_Auvergne_protocol_script_mode_setting_up_the_spin_systems.html

and the following pages.  If you do not have protons in your PDB file,
you'll need to generate them with external software (Molmol, Pymol,
etc.).  Unfortunately I haven't implemented a structure.attach_protons
user function yet, as I never found the citation for an algorithm to
correctly place protons in an X-ray structure.  And I know that the
calculated positions are not always the same for different software
programs, so it would be good to implement a number of the algorithms
so that there is a choice.

Regards,

Edward

Re: model free analysis: spin deselection problem

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