On 19 November 2015 at 13:03, Alain Oregioni <alain.oregi...@crick.ac.uk> 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
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