Re: Is there a command for opening an auto analysis for a pipe? -- June 06, 2013

I can see that I'm loosing you, so I've created the system test to
catch the bug you see:

http://article.gmane.org/gmane.science.nmr.relax.scm/17668
http://article.gmane.org/gmane.science.nmr.relax.scm/17670
http://article.gmane.org/gmane.science.nmr.relax.scm/17674

I've also fixed the bug:

http://article.gmane.org/gmane.science.nmr.relax.scm/17672
http://article.gmane.org/gmane.science.nmr.relax.scm/17676

This has all been merged into the relax_disp branch using svnmerge.py.
 The approach for extracting the user function commands from the log
is correct and will work in all cases.

As for opening the relaxation dispersion tab at start up, this is not
possible.  However you can have the same affect by opening a
previously saved state just after you launch relax.  If you are
repeating an operation often, then you can save a state just prior to
the repetitive operation and then load that the next time.  This saves
a lot of time.

For the number of integration points when performing volume
integration, this is quite important to know for the analysis of the
peak intensity errors.  This is not an issue if you have replicated
spectra though, as it is only used to propagate the baseplane RMSD
measurements.  Note that this is not implemented in relax yet, but in
the 12 years of relax's existence, no use has asked for this feature
(which is relatively trivial to implement).  Also the
spectrum.integration_points page should be skipped in the GUI peak
intensity wizard if you have replicated spectra.  I have just fixed
this too:

http://article.gmane.org/gmane.science.nmr.relax.scm/17678

I hope this will allow you to load your data.  Most people normally
measure peak heights (I do this in Sparky) and then load the Sparky,
NMRView, or XEasy peak lists one at a time, so these issues have not
been encountered before.  Or at least they have never been reported to
the relax mailing lists.  These are quite minor though and now should
be fixed.  Thank you for creating the bug report
https://gna.org/bugs/?20873, that allowed me to create a system test
and fix these problems, and importantly to make sure they never return
in the future.

Cheers,

Edward



On 6 June 2013 19:57, Troels Emtekær Linnet <tlinnet@xxxxxxxxx> wrote:

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?

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