Re: Custom Peak intensity reading -- June 06, 2013 - 16:33

On a different note, if you notice anywhere in relax's execution where
the messages are not informative enough, are misleading, or where
additional messages would be useful, these can all be reported as
bugs.  Anything in relax that causes confusion should be considered a
bug which should be fixed.

Regards,

Edward



On 6 June 2013 15:26, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> Oh, right, I see the problem.  This user function currently only has
> partial support for simultaneously loading all spectral data at once.
> The current way to do this is to change the spectrum ID and intensity
> column one-by-one while clicking on 'Apply' as you go.  But I have
> partly designed this user function to handle this situation, according
> to the user function documentation:
>
> "Generic intensity file:  This is a generic format which can be
> created by scripting to support non-supported peak lists.  It should
> contain in the first few columns enough information to identify the
> spin.  This can include columns for the molecule name, residue number,
> residue name, spin number, and spin name.  Alternatively a spin ID
> string column can be used. The peak intensities can be placed in
> another column specified by the integration column number.
> Intensities from multiple spectra can be placed into different
> columns, and these can then be specified simultaneously by setting the
> integration column value to a list of columns.  This list must be
> matched by setting the spectrum ID to a list of the same length..."
>
> Could you submit a bug report for this, attaching any files required
> to replicate the bug?  It would be useful to give a link to the Gmane
> archive as well (going to
> http://dir.gmane.org/gmane.science.nmr.relax.user -> clicking on
> "using frames and threads" -> finding message -> clicking on "<<<
> [thread] >>>" down the botton -> and copying the link).  I could then
> turn the instructions into a relax script, and incorporate both the
> script and data files into the test suite directories and create a
> system test to catch the bug.  Or, if you wish, as a learning exercise
> for becoming a relax developer you could give this a go yourself after
> creating the report.  This would all go into the relax trunk, and then
> be ported to the relax_disp branch using svnmerge.py.
>
> Cheers,
>
> Edward
>
>
>
> On 6 June 2013 15:04, Troels Emtekær Linnet <tlinnet@xxxxxxxxx> wrote:
> > I think it is because that:
> > spectrum_id='(2,6)'
> >
> > is translated to a string.
> >
> > Could it be corrected, so it does similar as:
> > int_col=(6, 7)
> >
> > Best
> > Troels Emtekær Linnet
> >
> >
> > 2013/6/6 Troels Emtekær Linnet <tlinnet@xxxxxxxxx>:
> > > Hi,
> > >
> > > No, not any luck.
> > > And, this time I am not renaming.
> > >
> > > Where can I find the longer error message?
> > > ---------
> > > Add spectra
> > > Click "Add"
> > >
> > > The file name = test.seq
> > > The Spectrum ID string: 2,0
> > > The Intensity column: 6,7
> > > ----------------
> > > protein 10 L 10 N 3.377659e+05 6.362446e+05
> > > protein 6 V 6 N 1.697771e+06 3.015788e+06
> > > protein 63 Y 63 N 8.673898e+05 1.726064e+06
> > > protein 4 Y 4 N 2.339480e+06 4.039142e+06
> > > protein 67 M 67 N 2.574062e+06 4.313824e+06
> > > protein 5 E 5 N 1.609356e+06 2.927111e+06
> > > protein 65 V 65 N 2.179341e+06 4.067343e+06
> > > protein 38 E 38 N 1.563795e+06 2.921316e+06
> > > protein 7 N 7 N 1.535896e+06 3.005234e+06
> > > protein 75 L 75 N 3.578841e+06 6.352595e+06
> > > ------------------------
> > >
> > > ----------
> > > relax> relax_disp.exp_type(exp_type='cpmg fixed')
> > > The fixed relaxation time period CPMG-type experiments.
> > >
> > > relax> 
> > > sequence.read(file='/sbinlab2/tlinnet/Desktop/ikn_20130510_S6wt_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/test.seq',
> > > 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)
> > > Opening the file
> > > '/sbinlab2/tlinnet/Desktop/ikn_20130510_S6wt_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/test.seq'
> > > for reading.
> > > # mol_name    res_num    res_name    spin_num    spin_name
> > > protein       10         L           10          N
> > > protein       6          V           6           N
> > > protein       63         Y           63          N
> > > protein       4          Y           4           N
> > > protein       67         M           67          N
> > > protein       5          E           5           N
> > > protein       65         V           65          N
> > > protein       38         E           38          N
> > > protein       7          N           7           N
> > > protein       75         L           75          N
> > >
> > > relax> 
> > > spectrum.read_intensities(file='/sbinlab2/tlinnet/Desktop/ikn_20130510_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/test.seq',
> > > dir=None, spectrum_id='2,0', heteronuc='N', proton='HN',
> > > int_method='height', int_col=(6, 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)
> > > Opening the file
> > > '/sbinlab2/tlinnet/Desktop/ikn_20130510_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/test.seq'
> > > for reading.
> > > Generic formatted data file.
> > >
> > > RelaxWarning: The sequence data in the line ['protein', '10', 'L',
> > > '10', 'N', '3.377659e+05', '6.362446e+05'] is invalid, the data is
> > > missing.
> > > RelaxWarning: The sequence data in the line ['protein', '6', 'V', '6',
> > > 'N', '1.697771e+06', '3.015788e+06'] is invalid, the data is missing.
> > > RelaxWarning: The sequence data in the line ['protein', '63', 'Y',
> > > '63', 'N', '8.673898e+05', '1.726064e+06'] is invalid, the data is
> > > missing.
> > > RelaxWarning: The sequence data in the line ['protein', '4', 'Y', '4',
> > > 'N', '2.339480e+06', '4.039142e+06'] is invalid, the data is missing.
> > > RelaxWarning: The sequence data in the line ['protein', '67', 'M',
> > > '67', 'N', '2.574062e+06', '4.313824e+06'] is invalid, the data is
> > > missing.
> > > RelaxWarning: The sequence data in the line ['protein', '5', 'E', '5',
> > > 'N', '1.609356e+06', '2.927111e+06'] is invalid, the data is missing.
> > > RelaxWarning: The sequence data in the line ['protein', '65', 'V',
> > > '65', 'N', '2.179341e+06', '4.067343e+06'] is invalid, the data is
> > > missing.
> > > RelaxWarning: The sequence data in the line ['protein', '38', 'E',
> > > '38', 'N', '1.563795e+06', '2.921316e+06'] is invalid, the data is
> > > missing.
> > > RelaxWarning: The sequence data in the line ['protein', '7', 'N', '7',
> > > 'N', '1.535896e+06', '3.005234e+06'] is invalid, the data is missing.
> > > RelaxWarning: The sequence data in the line ['protein', '75', 'L',
> > > '75', 'N', '3.578841e+06', '6.352595e+06'] is invalid, the data is
> > > missing.
> > > RelaxError: No corresponding data could be found within the file.
> > >
> > > -------------------------------
> > >
> > > Troels Emtekær Linnet
> > >
> > >
> > > 2013/6/6 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > > Hi,
> > > >
> > > > Have you had any luck finding the problem?  I would guess that this
> > > > doesn't work as the protein was renamed to something different to that
> > > > of the data file, hence you would see messages such as:
> > > >
> > > > relax> spectrum.read_intensities(file='test.seq', dir=None,
> > > > spectrum_id=None, heteronuc='N', proton='HN', int_method='height',
> > > > 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, int_col=6, sep=None,
> > > > spin_id=None, ncproc=None)
> > > > Opening the file '/data/edau/relax/branches/relax_disp/test.seq' for 
> > > > reading.
> > > > Generic formatted data file.
> > > >
> > > > RelaxWarning: Cannot find the spin #protein:10@N within the sequence.
> > > > RelaxWarning: Cannot find the spin #protein:6@N within the sequence.
> > > > RelaxWarning: Cannot find the spin #protein:63@N within the sequence.
> > > > RelaxWarning: Cannot find the spin #protein:4@N within the sequence.
> > > > RelaxWarning: Cannot find the spin #protein:67@N within the sequence.
> > > > RelaxWarning: Cannot find the spin #protein:5@N within the sequence.
> > > > RelaxWarning: Cannot find the spin #protein:65@N within the sequence.
> > > > RelaxWarning: Cannot find the spin #protein:38@N within the sequence.
> > > > RelaxWarning: Cannot find the spin #protein:7@N within the sequence.
> > > > RelaxWarning: Cannot find the spin #protein:75@N within the sequence.
> > > > RelaxError: No data could be loaded from the peak list
> > > >
> > > > I tried this by copying the data in your post to a file and following
> > > > the instructions.  This is normal as the molecule with the name
> > > > 'protein' no longer exists in the relax data store.  Or did you see
> > > > something different?  The RelaxError text you wrote about is slightly
> > > > different.
> > > >
> > > > Regards,
> > > >
> > > > Edward
> > > >
> > > >
> > > > On 4 June 2013 15:10, Edward d'Auvergne <edward.dauvergne@xxxxxxxxx> 
> > > > wrote:
> > > > > I have to admit, the error message should be made more informative!
> > > > > However that error statement (line 668 of lib/io.py) cannot be reached
> > > > > without relax giving many warnings.  The only possibility of reaching
> > > > > the error without warnings is if the file is empty.  Do you see
> > > > > warnings which could indicate the problem?  If not, I would suggest
> > > > > creating a bug report for the problem and attaching a minimal set of
> > > > > files to be able to reproduce the issue.  It would be best if the
> > > > > files are truncated to 1-2 spins (and maybe randomised if the data is
> > > > > to be kept secret).  If it really is a bug, then these files could be
> > > > > be added to the test suite and turned into a system or GUI test to
> > > > > catch the problem.
> > > > >
> > > > > Cheers,
> > > > >
> > > > > Edward
> > > > >
> > > > >
> > > > > On 4 June 2013 14:37, Troels Emtekær Linnet <tlinnet@xxxxxxxxx> wrote:
> > > > > > Hi.
> > > > > >
> > > > > > I have made a custom intensity peak/model file, for easy import in 
> > > > > > relax.
> > > > > > The form is:
> > > > > >
> > > > > > protein 10 L 10 N 3.377659e+05 6.362446e+05
> > > > > > protein 6 V 6 N 1.697771e+06 3.015788e+06
> > > > > > protein 63 Y 63 N 8.673898e+05 1.726064e+06
> > > > > > protein 4 Y 4 N 2.339480e+06 4.039142e+06
> > > > > > protein 67 M 67 N 2.574062e+06 4.313824e+06
> > > > > > protein 5 E 5 N 1.609356e+06 2.927111e+06
> > > > > > protein 65 V 65 N 2.179341e+06 4.067343e+06
> > > > > > protein 38 E 38 N 1.563795e+06 2.921316e+06
> > > > > > protein 7 N 7 N 1.535896e+06 3.005234e+06
> > > > > > protein 75 L 75 N 3.578841e+06 6.352595e+06
> > > > > >
> > > > > > This goes fine for model import, with standard settings.
> > > > > >
> > > > > > Start new analysis
> > > > > > Relaxation dispersion analysis
> > > > > > Relaxation dispersion experiment type selection
> > > > > > CPMG, fixed time
> > > > > > Data pipe set up
> > > > > > The starting data pipe for the analysis = origin - relax_disp (Mon Jun
> > > > > > 3 17:08:30 2013)
> > > > > > The data pipe bundle = relax_disp (Mon Jun 3 17:08:30 2013)
> > > > > >
> > > > > > Click: Spin editor
> > > > > > Click: Load spins
> > > > > > Make a test file: test.seq
> > > > > >
> > > > > > Click: From a file containing sequence data
> > > > > > The file name = test.seq
> > > > > > The spin ID string = Leave empty
> > > > > > Free format
> > > > > > Molecule name column (mol_name_col) = 1
> > > > > > Residue number column (res_num_col) = 2
> > > > > > Residue name column (res_name_col) = 3
> > > > > > Spin number column (spin_num_col) = 4
> > > > > > Spin name column (spin_name_col) = 5
> > > > > > You can then rename molecule by, right click "Molecule: protein",
> > > > > > "Name the molecule", Set "The new molecule name" to for example
> > > > > > "Test". Apply, then OK.
> > > > > >
> > > > > > Add spectra
> > > > > > Click "Add"
> > > > > >
> > > > > > The file name = test.seq
> > > > > > The Spectrum ID string: 2,0
> > > > > > The Intensity column: 6,7
> > > > > > rest is default
> > > > > >
> > > > > > Error:
> > > > > > No corresponding data could be found within the file.
> > > > > >
> > > > > > I can import single wise.
> > > > > >
> > > > > > best
> > > > > > Troels
> > > > > >
> > > > > >
> > > > > > Troels Emtekær Linnet
> > > > > >
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