Hi Lusine,
Welcome to the relax mailing lists! The problem you have encountered
is simply that for the spin systems you are looking at, that they have
no relaxation data loaded for them. I can only guess as I don't have
the information, but if you look back in the relax messages, you will
see that at the point of the relax_data.read() user function calls,
there will be warnings present there and no relaxation data will be
visible. Normally it should look something like:
-----
relax> relax_data.read(ri_id='R1_900', ri_type='R1', frq=900000000.0,
file='r1.900.out',
dir='/data/relax/branches/relax_disp/test_suite/shared_data/model_free/sphere/',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None,
spin_id=None)
RelaxWarning: The precise spectrometer frequency should be suppled, a
value such as 500000000 or 5e8 for a 500 MHz machine is not
acceptable. Please see the 'sfrq' parameter in the Varian procpar
file or the 'SFO1' parameter in the Bruker acqus file.
Opening the file
'/data/relax/branches/relax_disp/test_suite/shared_data/model_free/sphere//r1.900.out'
for reading.
RelaxWarning: The precise spectrometer frequency should be suppled, a
value such as 500000000 or 5e8 for a 500 MHz machine is not
acceptable. Please see the 'sfrq' parameter in the Varian procpar
file or the 'SFO1' parameter in the Bruker acqus file.
The following 900.0 MHz R1 relaxation data with the ID 'R1_900' has
been loaded into the relax data store:
# Spin_ID Value Error
#sphere_mol1:1@N 0.7111820201079988 0.014223640402159976
#sphere_mol1:2@N 0.7111820201079988 0.014223640402159976
#sphere_mol1:3@N 0.7111820201079988 0.014223640402159976
#sphere_mol1:4@N 0.7111820201079988 0.014223640402159976
#sphere_mol1:5@N 0.7111820201079988 0.014223640402159976
#sphere_mol1:6@N 0.7111820201079988 0.014223640402159976
#sphere_mol1:7@N 0.7111820201079988 0.014223640402159976
#sphere_mol1:8@N 0.7111820201079988 0.014223640402159976
#sphere_mol1:9@N 0.7111820201079988 0.014223640402159976
#sphere_mol1:9@NE1 0.7111820201079988 0.014223640402159976
-----
This is synthetic, perfect data from the relax test suite, so your
messages will be slightly different. I would also recommend that you
carefully look at all of the messages from the very start. Every
single warning must be thoroughly checked. I cannot emphasis this
enough! Some warnings will be acceptable, for example if there is
strange or missing data in a file (unassigned peaks, etc.). But
others will indicate problems that will later on be fatal for the
analysis. I hope this helps.
Regards,
Edward
On 24 July 2013 02:47, Simonyan, Lusine <lusine.simonyan.948@xxxxxxxxxxx>
wrote:
---------- Forwarded message ----------
From: Simonyan, Lusine <lusine.simonyan.948@xxxxxxxxxxx>
Date: Tue, Jul 23, 2013 at 9:52 AM
Subject: Over-fit spin deselection error
To: relax-announce@xxxxxxx
Hi,
I am trying to analyse ssNOE, R1, and R2 data for 600 and 800MHz using
relax, but for some reason I get a relax warning looking like this:
Over-fit spin deselection:
RelaxWarning: The spin '#hRGS4:4@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:5@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:6@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:7@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:8@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:9@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:10@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:11@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:12@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:13@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:14@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:15@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:16@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:17@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:18@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:19@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:20@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:21@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:22@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:23@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:24@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:25@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:26@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:27@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:28@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:29@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:30@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:31@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:32@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:33@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:34@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:35@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:36@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:37@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:38@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:39@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:40@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:41@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:42@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:43@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:44@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:45@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:48@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:51@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:52@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:53@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:54@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:55@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:56@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:57@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:60@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:61@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:62@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:64@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:65@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:66@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:67@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:68@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:69@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:70@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:71@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:72@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:73@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:74@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:75@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:76@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:77@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:78@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:79@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:81@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:82@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:83@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:84@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:85@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:86@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:87@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:88@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:89@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:90@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:91@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:92@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:93@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:94@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:95@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:96@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:97@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:99@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:100@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:101@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:102@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:103@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:104@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:105@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:106@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:107@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:108@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:109@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:110@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:111@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:112@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:113@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:114@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:115@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:116@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:117@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:118@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:119@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:120@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:121@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:122@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:123@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:124@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:125@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:126@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:127@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:128@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:129@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:130@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:131@N' has been deselected because of
insufficient data.
RelaxWarning: The spin '#hRGS4:132@N' has been deselected because of
insufficient data.
relax> value.write(param='noe', file='noe.600.out',
dir='/home/crowlab/NMR_data/
hRGS4_NMR/Dynamics/Dynamics_Agnes600_Feb2013/ssNOE_hRGS4_Feb2013/nv_data',
scaling=1.0, comment=None, bc=False, force=True)
Opening the file
'/home/crowlab/NMR_data/hRGS4_NMR/Dynamics/Dynamics_Agnes600_Feb2013/ssNOE_hRGS4_Feb2013/nv_data/noe.600.out'
for writing.
relax> results.write(file='results',
dir='/home/crowlab/NMR_data/hRGS4_NMR/Dynamics/Dynamics_Agnes600_Feb2013/ssNOE_hRGS4_Feb2013/nv_data',
compress_type=1, force=True)
Opening the file
'/home/crowlab/NMR_data/hRGS4_NMR/Dynamics/Dynamics_Agnes600_Feb2013/ssNOE_hRGS4_Feb2013/nv_data/results.bz2'
for writing.
relax> grace.write(x_data_type='spin', y_data_type='ref', spin_id=None,
plot_data='value', file='ref.agr',
dir='/home/crowlab/NMR_data/hRGS4_NMR/Dynamics/Dynamics_Agnes600_Feb2013/ssNOE_hRGS4_Feb2013/nv_data/grace',
force=True, norm=False)
Opening the file
'/home/crowlab/NMR_data/hRGS4_NMR/Dynamics/Dynamics_Agnes600_Feb2013/ssNOE_hRGS4_Feb2013/nv_data/grace/ref.agr'
for writing.
RelaxWarning: No data could be found, creating an empty file.
relax> grace.write(x_data_type='spin', y_data_type='sat', spin_id=None,
plot_data='value', file='sat.agr',
dir='/home/crowlab/NMR_data/hRGS4_NMR/Dynamics/Dynamics_Agnes600_Feb2013/ssNOE_hRGS4_Feb2013/nv_data/grace',
force=True, norm=False)
Opening the file
'/home/crowlab/NMR_data/hRGS4_NMR/Dynamics/Dynamics_Agnes600_Feb2013/ssNOE_hRGS4_Feb2013/nv_data/grace/sat.agr'
for writing.
RelaxWarning: No data could be found, creating an empty file.
I have tried modifying the pdb file, but still I get the same warning no
matter. I don't know how to fix this problem, please help me if it is
possible. I also went through the archive messages and I saw someone else
was encountering with similar problem and the reply message mentioned that
the latest version of relax has solved the bug. However, I am using the
latest version of relax, and still come across with the RelaxWarning.
Thanks,
Lusine Simonyan
Biochemistry Undergraduate Student,
California State University, Northridge.
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Re: Over-fit spin deselection error