On Thursday, 20 June 2019, Yulian Gavrilov <[email protected]>
wrote:
> 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)
>
>
Hi Yulian,
Welcome to the relax mailing lists! As your question is frequently asked,
I have extensively documented this area of analysis with the different
combinations of peak height vs. volume to RMSD baseplane vs. replicated
spectra:
https://www.nmr-relax.com/manual/spectrum_error_analysis.html
Please have a careful read. If this doesn't help, please ask again here.
Regards,
Edward
_______________________________________________
nmr-relax-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/nmr-relax-users
