Dear Edward, Thank you for your reply! I checked my input and my script. Probably I am missing something but unfortunately, I cannot understand the reason for the error. If I keep only the volumes in my Sparky input file (and remove the hights) relax does not load any intensities at all. Yulian
On Sat, Jun 22, 2019, 09:21 Edward d'Auvergne <[email protected]> wrote: > 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 >
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