Hi Edward.
Well, it doesn't solve my problem.
I really just would like to get this program running soon. :-)
I have not been able to run anything until now, and it eats my time...
(But if I can get it to work, then I hopefully can save time).
So, I have made a "relax" script generator, which defines all the
things relax needs.
But I don't know what it needs, before I run the GUI, and go through the
steps.
Then I parse the necessary information into my script generator, which
makes the
relax script.
So at the moment, I run the gui with the logfile, and try to figure
out, how can I put
that command into my script generator.
And it would be "nice", but not necessary, if it could "pop" up the
"Relaxation dispersion" tab, when
I open the relax -g.
I think I need one more thing to know.
--
spectrum.integration_points
--
I have used summation over spectrum points with a box of size +/-1
point in dx and dx.
How, can I, should I, then set number of points to 9 ? Or just leave it be?
spectrum.integration_points(N=9, spectrum_id='0_2', spin_id=None)
-----------------------------------------------------
# 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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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')
spectrum.read_intensities(file='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/table_ser_files_model.txt',
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=0.0)
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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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='/sbinlab2/tlinnet/Desktop/ikn_20130510_prot_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/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
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',])
2013/6/6 Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>:
Hi,
This concept does not apply to the prompt/script UIs. Instead you
just create the data pipe and execute the relevant user functions
(non-relevant ones should give intelligible error messages). For the
auto-analysis in this UI mode, you need to set up a base data pipe
containing all of the data you will need for the analysis, and then
send that into the auto-analysis which was imported at the start of
the script. See the file
sample_scripts/model_free/dauvergne_protocol.py for an example.
If you are referring to bug #20873 (https://gna.org/bugs/?20873), then
the auto-analysis is not needed at all. This just requires a few user
function calls on a data pipe, set to maybe 'relax_fit', to trigger
the issue. I hope this answers your question.
Regards,
Edward
On 6 June 2013 18:48, Troels Emtekær Linnet <tlinnet@xxxxxxxxx> wrote:
I can do it by:
Ctrl+D
Right click, Associate with a new auto analysis
Is there a relax command to open this?
best
Troels Emtekær Linnet
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Re: Is there a command for opening an auto analysis for a pipe?