Hi Edward,
Thank you very much for your reply; I'm glad it's a simple error. I'll add
protons to the PDB.
If I may say, it would be nice to have a simple way of doing it in the script, even
roughly for a start: if it "works" with a sequence, it wouldn't be worse to
do it with a PDB without H (add any warning necessary in the description).
Hopefully, things will go smoothly for me from now on...
This mailing list is very useful. keep it alive!
Best wishes,
Alain.
On 19/11/2015 12:47, Edward d'Auvergne wrote:
On 19 November 2015 at 13:03, Alain Oregioni
<Alain.Oregioni@xxxxxxxxxxx><mailto: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
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Re: model free analysis: spin deselection problem