Hi Dhanas,
For reference in the mailing list archives
(http://thread.gmane.org/gmane.science.nmr.relax.user/1543), the bug
report is located at https://gna.org/bugs/?21562. To catch this bug,
I will create a relax system test. This will consist of:
- A truncated data set. I think I'll take your data for residues :12,
:13, and :14, and delete all other data from the peak lists and PDB
files.
- A simple relax script to perform the analysis. I will just copy the
user functions from the relax log messages you posted at
http://thread.gmane.org/gmane.science.nmr.relax.user/1543 (now in the
text file https://gna.org/bugs/download.php?file_id=19920 attached to
bug #21562). That is everything starting with "relax>", i.e.:
pipe.create('NOE fail', 'noe')
structure.read_pdb(file='2AT7_fmf.pdb')
structure.load_spins(spin_id='@N', mol_name_target=None, ave_pos=True)
spectrum.read_intensities(file='n_np4_hs_ph65_02mm_noe1.list',
dir=None, spectrum_id='no1', dim=1, int_method='height', int_col=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, ncproc=None)
noe.spectrum_type(spectrum_type='ref', spectrum_id='no1')
spectrum.read_intensities(file='n_np4_hs_ph65_02mm_noe2.list',
dir=None, spectrum_id='no2', dim=1, int_method='height', int_col=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, ncproc=None)
spectrum.replicated(spectrum_ids=['no2', 'no1'])
noe.spectrum_type(spectrum_type='ref', spectrum_id='no2')
spectrum.read_intensities(file='y_np4_hs_ph65_02mm_noe1.list',
dir=None, spectrum_id='yes1', dim=1, int_method='height',
int_col=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, ncproc=None)
noe.spectrum_type(spectrum_type='sat', spectrum_id='yes1')
spectrum.read_intensities(file='y_np4_hs_ph65_02mm_noe2.list',
dir=None, spectrum_id='yes2', dim=1, int_method='height',
int_col=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, ncproc=None)
spectrum.replicated(spectrum_ids=['yes2', 'yes1'])
noe.spectrum_type(spectrum_type='sat', spectrum_id='yes2')
spectrum.error_analysis(subset=None)
calc(verbosity=1)
value.write(param='noe', file='noe.600.out', dir='.', scaling=1.0,
comment=None, bc=False, force=True)
results.write(file='results', dir='.', compress_type=1, force=True)
grace.write(x_data_type='res_num', y_data_type='ref', spin_id=None,
plot_data='value', file='ref.agr', dir='.', force=True, norm=False)
grace.write(x_data_type='res_num', y_data_type='sat', spin_id=None,
plot_data='value', file='sat.agr', dir='.', force=True, norm=False)
grace.write(x_data_type='res_num', y_data_type='noe', spin_id=None,
plot_data='value', file='noe.agr', dir='.', force=True, norm=False)
I added two user functions at the start as the log was not all there.
The directories have all been changed as well. This script triggers
the error, and it can be seen that it is independent of the GUI and
operating system. Using the Mac OS X dmg distribution running scripts
from the terminal is not possible, but you can use the 'script' user
function from the user function menus to run it. Once the test is
functional, it should be easy to find the problem and fix it.
Cheers,
Edward
On 30 January 2014 17:53, Dhanasekaran Muthu <dhanas@xxxxxxxxxxxxxxxxx>
wrote:
Hi Edward,
Thanks for your prompt response.I will submit a bug report as you have
described. This is the problem on Linux version also. The noe.out
produces null values.
Dhanas
DhanasOn Jan 30, 2014, at 9:02 AM, Edward d'Auvergne
<edward@xxxxxxxxxxxxx> wrote:
Hi Dhanas,
The problem you are seeing is actually because of the relax warnings
starting at:
RelaxWarning: The spin '#2AT7_fmf_mol1:3@N' has been deselected
because of insufficient data.
From looking at the other messages, I am unsure as to why this is not
working. To help solve this problem would you be able to submit a bug
report (https://gna.org/bugs/?func=additem&group=relax)? Cheers! If
you could attach to that bug report all of the input files as well as
a description of all steps you took to produce the error, that would
be appreciated (you can truncate the files and maybe randomise the
heights if you would like keep the data private for now). It would
also be good if you could attach a file with the entire contents of
the relax controller window. If I am able to use your data and
reproduce the bug, then I should be able to fix this problem within a
few minutes.
Cheers,
Edward
P. S. Note that for a public mailing list, it is best not to attach
any files. The relax bug, task, and support request trackers are
where files should be uploaded.
On 29 January 2014 21:55, Dhanasekaran Muthu <dhanas@xxxxxxxxxxxxxxxxx>
wrote:
Hi,
I am using Relax Ver 3.1.3 on Mac OS. It worked beautifully to
calculate the R1 and R2 values using replicated spectra to get the
error. But it fails to calculate NOE if I use replicated spectra for
error. It produces empty NOE.out file. However it works fine if I just
use only one set of data(saturated and reference) and baseplane RMSD
for error calculation.
Please let me know if any of you faced this problem and how you solved
this issue.
Thanks,
Dhanas
Here is the log copied from the controller: (the detailed one is
attached in this E-mail)
relax> value.write(param='noe', file='noe.600.out',
dir='/Users/Dhanas/Desktop/relax.app/Contents/Resources', scaling=1.0,
comment=None, bc=False, force=True)
Opening the file
'/Users/Dhanas/Desktop/relax.app/Contents/Resources/noe.600.out' for
writing.
relax> results.write(file='results',
dir='/Users/Dhanas/Desktop/relax.app/Contents/Resources',
compress_type=1, force=True)
Opening the file
'/Users/Dhanas/Desktop/relax.app/Contents/Resources/results.bz2' for
writing.
relax> grace.write(x_data_type='res_num', y_data_type='ref',
spin_id=None, plot_data='value', file='ref.agr',
dir='/Users/Dhanas/Desktop/relax.app/Contents/Resources/grace',
force=True, norm=False)
Opening the file
'/Users/Dhanas/Desktop/relax.app/Contents/Resources/grace/ref.agr' for
writing.
RelaxWarning: No data could be found, creating an empty file.
relax> grace.write(x_data_type='res_num', y_data_type='sat',
spin_id=None, plot_data='value', file='sat.agr',
dir='/Users/Dhanas/Desktop/relax.app/Contents/Resources/grace',
force=True, norm=False)
Opening the file
'/Users/Dhanas/Desktop/relax.app/Contents/Resources/grace/sat.agr' for
writing.
RelaxWarning: No data could be found, creating an empty file.
relax> grace.write(x_data_type='res_num', y_data_type='noe',
spin_id=None, plot_data='value', file='noe.agr',
dir='/Users/Dhanas/Desktop/relax.app/Contents/Resources/grace',
force=True, norm=False)
Opening the file
'/Users/Dhanas/Desktop/relax.app/Contents/Resources/grace/noe.agr' for
writing.
RelaxWarning: No data could be found, creating an empty file.
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Re: NOE analysis issue