Dear all,
Please can you suggest me a working version of noe.py with Sparky input
with volume based intensities?
The script works for me with hight based intensities but not with volume
based intensities.
In my case (relax-4.0.3):
- the script loads into relax hight intensities instead of volume
intensities;
- the script returns this error: RelaxError: This has not yet been
implemented for the current data pipe.
Thank you!
My Sparky input:
Assignment w1 w2 Height Volume
F50N-F50HN 122.783 9.077 5.17E+08 2.58E+09
V13N-V13HN 121.553 8.506 7.24E+08 3.20E+09
....
My noe.py:
# Create the NOE data pipe.
pipe.create('NOE', 'noe')
# Load the backbone amide 15N spins from a PDB file.
structure.read_pdb('test.pdb')
structure.load_spins(spin_id='@N')
#structure.load_spins(spin_id='@NE1')
# Load the reference spectrum and saturated spectrum peak intensities.
spectrum.read_intensities(file='NOE1_750_hight_vol1.list', spectrum_id=
'ref_ave', int_method='point sum', int_col=4)
spectrum.read_intensities(file='NOE2_750_hight_vol1.list', spectrum_id=
'sat_ave', int_method='point sum', int_col=4)
#spectrum.read_intensities(file='NOE1_750_hight', spectrum_id='ref_ave')
#spectrum.read_intensities(file='NOE2_750_hight', spectrum_id='sat_ave')
# Set the spectrum types.
noe.spectrum_type('ref', 'ref_ave')
noe.spectrum_type('sat', 'sat_ave')
# Set the errors.
spectrum.baseplane_rmsd(error=2.768E+06, spectrum_id='ref_ave')
spectrum.baseplane_rmsd(error=8.963E+06, spectrum_id='sat_ave')
# Individual residue errors.
#spectrum.baseplane_rmsd(error=122000, spectrum_id='ref_ave',
spin_id=":114")
#spectrum.baseplane_rmsd(error=8500, spectrum_id='sat_ave', spin_id=":114")
# Peak intensity error analysis.
spectrum.integration_points(N=9, spectrum_id='ref_ave')
spectrum.integration_points(N=9, spectrum_id='sat_ave')
spectrum.error_analysis()
# Deselect unresolved residues.
#deselect.read(file='unresolved', mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5)
# Calculate the NOEs.
minimise.calculate()
# Save the NOEs.
value.write(param='noe', file='noe.out', force=True)
# Create grace files.
grace.write(y_data_type='peak_intensity', file='intensities.agr', force=True
)
grace.write(y_data_type='noe', file='noe.agr', force=True)
# View the grace files.
grace.view(file='intensities.agr')
grace.view(file='noe.agr')
# Write the results.
results.write(file='results', dir=None, force=True)
# Save the program state.
state.save('save', force=True)
Regards,
Yulian Gavrilov
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