Difference between revisions of "Sherekhan"

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spectrometer.frequency(id='0_2', frq=750.0614444, units='MHz')
 
spectrometer.frequency(id='0_2', frq=750.0614444, units='MHz')
  
spectrum.read_intensities(file='table_ser_files_model.txt',
+
### Repeat for loading all intensity files
dir=None, spectrum_id='1_0', heteronuc='N', proton='HN', int_method='point sum', int_col=(7), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='1_0', cpmg_frq=None)
 
relax_disp.relax_time(spectrum_id='1_0', time=0.05)
 
spectrometer.frequency(id='1_0', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='2_8', heteronuc='N', proton='HN', int_method='point sum', int_col=(8), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='2_8', cpmg_frq=160.0)
 
relax_disp.relax_time(spectrum_id='2_8', time=0.05)
 
spectrometer.frequency(id='2_8', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='3_30', heteronuc='N', proton='HN', int_method='point sum', int_col=(9), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='3_30', cpmg_frq=600.0)
 
relax_disp.relax_time(spectrum_id='3_30', time=0.05)
 
spectrometer.frequency(id='3_30', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='4_4', heteronuc='N', proton='HN', int_method='point sum', int_col=(10), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='4_4', cpmg_frq=80.0)
 
relax_disp.relax_time(spectrum_id='4_4', time=0.05)
 
spectrometer.frequency(id='4_4', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='5_42', heteronuc='N', proton='HN', int_method='point sum', int_col=(11), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='5_42', cpmg_frq=840.0)
 
relax_disp.relax_time(spectrum_id='5_42', time=0.05)
 
spectrometer.frequency(id='5_42', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='6_6', heteronuc='N', proton='HN', int_method='point sum', int_col=(12), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='6_6', cpmg_frq=120.0)
 
relax_disp.relax_time(spectrum_id='6_6', time=0.05)
 
spectrometer.frequency(id='6_6', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='7_2', heteronuc='N', proton='HN', int_method='point sum', int_col=(13), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='7_2', cpmg_frq=40.0)
 
relax_disp.relax_time(spectrum_id='7_2', time=0.05)
 
spectrometer.frequency(id='7_2', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='8_30', heteronuc='N', proton='HN', int_method='point sum', int_col=(14), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='8_30', cpmg_frq=600.0)
 
relax_disp.relax_time(spectrum_id='8_30', time=0.05)
 
spectrometer.frequency(id='8_30', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='9_46', heteronuc='N', proton='HN', int_method='point sum', int_col=(15), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='9_46', cpmg_frq=920.0)
 
relax_disp.relax_time(spectrum_id='9_46', time=0.05)
 
spectrometer.frequency(id='9_46', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='10_10', heteronuc='N', proton='HN', int_method='point sum', int_col=(16), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='10_10', cpmg_frq=200.0)
 
relax_disp.relax_time(spectrum_id='10_10', time=0.05)
 
spectrometer.frequency(id='10_10', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='11_18', heteronuc='N', proton='HN', int_method='point sum', int_col=(17), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='11_18', cpmg_frq=360.0)
 
relax_disp.relax_time(spectrum_id='11_18', time=0.05)
 
spectrometer.frequency(id='11_18', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='12_26', heteronuc='N', proton='HN', int_method='point sum', int_col=(18), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='12_26', cpmg_frq=520.0)
 
relax_disp.relax_time(spectrum_id='12_26', time=0.05)
 
spectrometer.frequency(id='12_26', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='13_38', heteronuc='N', proton='HN', int_method='point sum', int_col=(19), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='13_38', cpmg_frq=760.0)
 
relax_disp.relax_time(spectrum_id='13_38', time=0.05)
 
spectrometer.frequency(id='13_38', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='14_2', heteronuc='N', proton='HN', int_method='point sum', int_col=(20), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='14_2', cpmg_frq=40.0)
 
relax_disp.relax_time(spectrum_id='14_2', time=0.05)
 
spectrometer.frequency(id='14_2', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='15_14', heteronuc='N', proton='HN', int_method='point sum', int_col=(21), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='15_14', cpmg_frq=280.0)
 
relax_disp.relax_time(spectrum_id='15_14', time=0.05)
 
spectrometer.frequency(id='15_14', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='16_14', heteronuc='N', proton='HN', int_method='point sum', int_col=(22), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='16_14', cpmg_frq=280.0)
 
relax_disp.relax_time(spectrum_id='16_14', time=0.05)
 
spectrometer.frequency(id='16_14', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='17_30', heteronuc='N', proton='HN', int_method='point sum', int_col=(23), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='17_30', cpmg_frq=600.0)
 
relax_disp.relax_time(spectrum_id='17_30', time=0.05)
 
spectrometer.frequency(id='17_30', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='18_22', heteronuc='N', proton='HN', int_method='point sum', int_col=(24), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='18_22', cpmg_frq=440.0)
 
relax_disp.relax_time(spectrum_id='18_22', time=0.05)
 
spectrometer.frequency(id='18_22', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='19_46', heteronuc='N', proton='HN', int_method='point sum', int_col=(25), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='19_46', cpmg_frq=920.0)
 
relax_disp.relax_time(spectrum_id='19_46', time=0.05)
 
spectrometer.frequency(id='19_46', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='20_14', heteronuc='N', proton='HN', int_method='point sum', int_col=(26), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='20_14', cpmg_frq=280.0)
 
relax_disp.relax_time(spectrum_id='20_14', time=0.05)
 
spectrometer.frequency(id='20_14', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='21_34', heteronuc='N', proton='HN', int_method='point sum', int_col=(27), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='21_34', cpmg_frq=680.0)
 
relax_disp.relax_time(spectrum_id='21_34', time=0.05)
 
spectrometer.frequency(id='21_34', frq=750.0614444, units='MHz')
 
 
 
spectrum.read_intensities(file='table_ser_files_model.txt',
 
dir=None, spectrum_id='22_46', heteronuc='N', proton='HN', int_method='point sum', int_col=(28), spin_id_col=None, mol_name_col=1,
 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
 
relax_disp.cpmg_frq(spectrum_id='22_46', cpmg_frq=920.0)
 
relax_disp.relax_time(spectrum_id='22_46', time=0.05)
 
spectrometer.frequency(id='22_46', frq=750.0614444, units='MHz')
 
  
 
# Replicated spectrums
 
# Replicated spectrums
Line 201: Line 49:
 
relax_disp.cluster(cluster_id='Sherekhan', spin_id=None)
 
relax_disp.cluster(cluster_id='Sherekhan', spin_id=None)
 
relax_disp.sherekhan_input(force=True, spin_id=None)
 
relax_disp.sherekhan_input(force=True, spin_id=None)
 
 
 
</source>
 
</source>

Revision as of 12:51, 13 June 2013

Online analysis tool

Homepage

Fitting functions

Use relax GUI to create input file

Use relax script to create input file

# Create the 'rx' data pipe.
pipe.create(pipe_name='origin rx', pipe_type='relax_disp', bundle='rx')

# The type of experiment
relax_disp.exp_type(exp_type='cpmg fixed')

# Read the sequence from file
sequence.read(file='table_ser_files_model.txt',
dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None)

# Read the intensities from columns
spectrum.read_intensities(file='table_ser_files_model.txt',
dir=None, spectrum_id='0_2', heteronuc='N', proton='HN', int_method='point sum', int_col=(6), spin_id_col=None, mol_name_col=1,
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
relax_disp.cpmg_frq(spectrum_id='0_2', cpmg_frq=40.0)
relax_disp.relax_time(spectrum_id='0_2', time=0.05)
spectrometer.frequency(id='0_2', frq=750.0614444, units='MHz')

### Repeat for loading all intensity files

# Replicated spectrums
spectrum.replicated(spectrum_ids=['0_2','7_2','14_2',])
spectrum.replicated(spectrum_ids=['15_14','16_14','20_14',])
spectrum.replicated(spectrum_ids=['3_30','8_30','17_30',])
spectrum.replicated(spectrum_ids=['9_46','19_46','22_46',])
# Spin isotope
spin.isotope(isotope='15N', spin_id='@N*', force=True)

# Make error analysis
spectrum.error_analysis(subset=['0_2', '1_0', '2_8', '3_30', '4_4', '5_42', '6_6', '7_2', '8_30', '9_46', '10_10', '11_18', '12_26', '13_38', '14_2', '15_14', '16_14', '17_30', '18_22', '19_46', '20_14', '21_34', '22_46'])

# The 'R2eff' model
pipe.copy(pipe_from='origin rx', pipe_to='R2eff', bundle_to='rx')
pipe.switch(pipe_name='R2eff')
relax_disp.select_model(model='R2eff')
calc(verbosity=1)

# Cluster all spin, and export to sherekhan
relax_disp.cluster(cluster_id='Sherekhan', spin_id=None)
relax_disp.sherekhan_input(force=True, spin_id=None)