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Today's Topics:
1. Re: About model-free analysis (Edward d'Auvergne)
2. Error message and test failures from the relax test suites
(Nicolas Doucet)
Message: 1
Date: Thu, 6 Sep 2012 14:14:19 +0200
From: "Edward d'Auvergne" <edward@xxxxxxxxxxxxx>
To: mengjun.xue@xxxxxxxxxxxxxxxxxxxx
Cc: relax-users@xxxxxxx
Subject: Re: About model-free analysis
Message-ID:
<CAED9pY_R8s31My1w19uh5ss7Cjhh6WJLEs62sUUHsF8SxeEc7g@xxxxxxxxxxxxxx>
Content-Type: text/plain; charset=ISO-8859-1
Hi Mengjun,
I've been looking for the relevant links as we have discussed this
topic a number of times on the relax-users mailing list. One good
reference would be to read all the messages sent by myself, Sebastien
Morin, Alex Hansen, Michael Marlow, and Gary Thompson in the thread
called "CSA & bond length" starting at:
http://thread.gmane.org/gmane.science.nmr.relax.user/192
and continued on the relax-devel mailing list at:
http://thread.gmane.org/gmane.science.nmr.relax.devel/1115
http://thread.gmane.org/gmane.science.nmr.relax.devel/1116
http://thread.gmane.org/gmane.science.nmr.relax.devel/1119
I'll keep looking for the other threads which discuss this, as this
was recently talked about, but I cannot find the messages right now.
In summary, for protein backbone NH data you should really use 1.02
Angstrom with -172 ppm CSA. The value of -160 ppm is from solid state
studies of peptides and is an underestimation for solution NMR.
There is CSA variability but the amount of variability is highly
debated. Some of Nico Tjandra's estimates of variability might be on
the high side, David Fushman's might be more reasonable. In reality,
no one really knows what the real CSA and bond length values are and
no one has reliably de-convoluted the internal ps-ns dynamics from
these parameters to be able to properly answer this question.
Therefore everyone takes the compromise of 1.02 A with roughly -172
ppm (the Hall and Fushman average value). There is another school of
thought from the NIH direction of Washington DC which says we should
use 1.04 A with -160 ppm. However this will generally shift the order
parameters higher and closer to one - causing the optimisation
algorithms to have severe problems and failures due to the convolution
of the optimisation space that this results in So it is not
recommended for a model-free analysis - the removal of zero-point
motions concept. As long as you are consistent and know that the
order parameters are a relative concept rather than absolute - then
you can compare different states. I hope this helps.
Regards,
Edward
P. S. If you do solve this problem reliably, you will probably
receive quite a few citations and make a name for yourself. However
the NMR field has being trying to solve this unsuccessfully for the
last who knows how many decades. So I wouldn't recommend trying
unless you have an incredible amount of spare time and don't mind
diving into the deepest depths of NMR and physics theory.
On 5 September 2012 18:09, <mengjun.xue@xxxxxxxxxxxxxxxxxxxx> wrote:
> Hi,
>
> When doing model-free analysis, NH bond length set to 1.02 angstrom
> normally, but it is a little bit different for different amino acid residue;
> and
> also the N chemical shift anisotropy set to say -160 ppm normally, but CSA
> is changing from residue to residue, How do Relax solve such kind of
> problem when doing model-free analysis?
>
> Regards,
>
> Mengjun Xue
>
>
>
>
>
>
> relax (http://www.nmr-relax.com)
>
> This is the relax-users mailing list
> relax-users@xxxxxxx
>
> To unsubscribe from this list, get a password
> reminder, or change your subscription options,
> visit the list information page at
> https://mail.gna.org/listinfo/relax-users
Message: 2
Date: Thu, 6 Sep 2012 14:44:32 -0400
From: Nicolas Doucet <nicolas.doucet@xxxxxxxxxxx>
To: Maddy Strickland <M.Strickland@xxxxxxxxxxxxx>
Cc: "relax-users@xxxxxxx" <relax-users@xxxxxxx>, Edward d'Auvergne
<edward@xxxxxxxxxxxxx>
Subject: Error message and test failures from the relax test suites
Message-ID: <4A76B296-631C-4395-8BB2-FB838FA833B3@xxxxxxxxxxx>
Content-Type: text/plain; charset="iso-8859-1"
Maddy,
Thanks a lot for your files. After deleting the output files, we tried to run your T1 'as is' to no avail. As you can see from the message below, we get an error very similar to the one we previously saw with our own files. It cannot find spins within the sequence. Can you really run the files you sent us without a single issue?
I'm starting to wonder whether our problem isn't related to software or module installation. Are you running relax on linux? We're running everything on Ubuntu 12.04 LTS with Python 2.7.3. We tried on 32-bit and 64-bit machines. No difference. I did install Python, NumPy, SciPy and wxPython as dependencies and the GUI also works fine when I boot it up. Perhaps I'm missing something.
Anyway, I also ran the relax test suites and I'm getting the following Monte Carlo failures:
System/functional tests:
FAIL: test_monte_carlo_sims (test_suite.system_tests.n_state_model.N_state_model)
Test the Monte Carlo simulation data of fitting RDCs and PCSs.
GUI tests:
FAIL: test_monte_carlo_sims (test_suite.gui_tests.n_state_model.N_state_model)
Test the Monte Carlo simulation data of fitting RDCs and PCSs.
The 'unit test' is fine. However, the error message we're getting here is clearly unrelated to any type of calculation. The software simply doesn't recognize spins, which could make sense considering they're not written the same way in your sequence.out and list files.
I'm a bit puzzled as to why it works for you and not for us.
Nick
--
Nicolas Doucet
Assistant Professor
INRS - Institut Armand-Frappier
University of Quebec
Institut Pasteur International Network
531 Boulevard des Prairies
Laval (Quebec) H7V 1B7 CANADA
Phone: (450) 687-5010 #4212
Fax: (450) 686-5501
Email: nicolas.doucet@xxxxxxxxxxx
Web: http://www.profs.inrs.ca/ndoucet/
--
Begin forwarded message:
>
> relax 2.1.0
>
> Molecular dynamics by NMR data analysis
>
> Copyright (C) 2001-2006 Edward d'Auvergne
> Copyright (C) 2006-2012 the relax development team
>
> This is free software which you are welcome to modify and redistribute under the conditions of the
> GNU General Public License (GPL). This program, including all modules, is licensed under the GPL
> and comes with absolutely no warranty. For details type 'GPL' within the relax prompt.
>
> Assistance in using the relax prompt and scripting interface can be accessed by typing 'help' within
> the prompt.
>
> Processor fabric: Uni-processor.
>
> script = 'T1_curve_fit.py'
>
> ###############################################################################
> # #
> # Copyright (C) 2004-2008 Edward d'Auvergne #
> # #
> # This file is part of the program relax. #
> # #
> # relax is free software; you can redistribute it and/or modify #
> # it under the terms of the GNU General Public License as published by #
> # the Free Software Foundation; either version 2 of the License, or #
> # (at your option) any later version. #
> # #
> # relax is distributed in the hope that it will be useful, #
> # but WITHOUT ANY WARRANTY; without even the implied warranty of #
> # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
> # GNU General Public License for more details. #
> # #
> # You should have received a copy of the GNU General Public License #
> # along with relax; if not, write to the Free Software #
> # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA #
> # #
> ###############################################################################
>
> # Script for relaxation curve fitting.
> ######################################
>
>
> # Create the 'rx' data pipe.
> pipe.create('rx', 'relax_fit')
>
> # Load sequence and spins
> sequence.read('sequence.out', spin_name_col=2)
>
> # Spectrum names.
> names = [
> 'T1_0111',
> 'T1_0333',
> 'T1_0555',
> 'T1_111',
> 'T1_1998',
> 'T1_333',
> 'T1_4995',
> 'T1_666',
> 'T1_888',
> ]
>
> # Relaxation times (in seconds).
> times = [
> 0.0111,
> 0.0333,
> 0.0555,
> 0.111,
> 0.1998,
> 0.333,
> 0.4995,
> 0.666,
> 0.888,
> ]
>
> # Loop over the spectra.
> for i in xrange(len(names)):
> # Load the peak intensities.
> spectrum.read_intensities(file=names[i]+'.list', spectrum_id=names[i], int_method='height')
>
> # Set the relaxation times.
> relax_fit.relax_time(time=times[i], spectrum_id=names[i])
>
> # Set the baseplane error
> spectrum.baseplane_rmsd(error=461070, spectrum_id='T1_0111')
> spectrum.baseplane_rmsd(error=437800, spectrum_id='T1_0333')
> spectrum.baseplane_rmsd(error=440440, spectrum_id='T1_0555')
> spectrum.baseplane_rmsd(error=426960, spectrum_id='T1_111')
> spectrum.baseplane_rmsd(error=376040, spectrum_id='T1_1998')
> spectrum.baseplane_rmsd(error=323600, spectrum_id='T1_333')
> spectrum.baseplane_rmsd(error=262310, spectrum_id='T1_4995')
> spectrum.baseplane_rmsd(error=212290, spectrum_id='T1_666')
> spectrum.baseplane_rmsd(error=164550, spectrum_id='T1_888')
>
> # Peak intensity error analysis.
> spectrum.error_analysis()
>
> # Deselect unresolved spins.
> deselect.read(file='unresolved')
>
> # Set the relaxation curve type.
> relax_fit.select_model('exp')
>
> # Grid search.
> grid_search(inc=11)
>
> # Minimise.
> minimise('simplex', scaling=False, constraints=False)
>
> # Monte Carlo simulations.
> monte_carlo.setup(number=500)
> monte_carlo.create_data()
> monte_carlo.initial_values()
> minimise('simplex', scaling=False, constraints=False)
> monte_carlo.error_analysis()
>
> # Save the relaxation rates.
> value.write(param='rx', file='rx.out', force=True)
>
> # Save the results.
> results.write(file='results', force=True)
>
> # Create Grace plots of the data.
> grace.write(y_data_type='rx', file='rx.agr', force=True) # Relaxation rate.
>
> # Display the Grace plots.
> grace.view(file='rx.agr')
>
> # Save the program state.
> state.save('rx.save', force=True)
>
>
> relax> pipe.create(pipe_name='rx', pipe_type='relax_fit', bundle=None)
>
> relax> sequence.read(file='sequence.out', dir=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=2, sep=None, spin_id=None)
> Opening the file 'sequence.out' for reading.
> # mol_name res_num res_name spin_num spin_name
> None None None None Res_name
> None None None None Trp
> None None None None Trp
> None None None None Ser
> None None None None Asn
> None None None None Ser
> None None None None Ser
> None None None None Ala
> None None None None Thr
> None None None None Pro
> None None None None Ile
> None None None None Val
> None None None None Gln
> None None None None Phe
> None None None None Gln
> None None None None Gly
> None None None None Glu
> None None None None Ser
> None None None None Asn
> None None None None Cys
> None None None None Leu
> None None None None Lys
> None None None None Cys
> None None None None Phe
> None None None None Arg
> None None None None Tyr
> None None None None Arg
> None None None None Leu
> None None None None Asn
> None None None None Asp
> None None None None Lys
> None None None None His
> None None None None Arg
> None None None None His
> None None None None Leu
> None None None None Phe
> None None None None Asp
> None None None None Leu
> None None None None Ile
> None None None None Ser
> None None None None Ser
> None None None None Thr
> None None None None Trp
> None None None None His
> None None None None Trp
> None None None None Ala
> None None None None Ser
> None None None None Pro
> None None None None Lys
> None None None None Ala
> None None None None Pro
> None None None None His
> None None None None Lys
> None None None None His
> None None None None Ala
> None None None None Ile
> None None None None Val
> None None None None Thr
> None None None None Val
> None None None None Thr
> None None None None Tyr
> None None None None His
> None None None None Ser
> None None None None Glu
> None None None None Glu
> None None None None Gln
> None None None None Arg
> None None None None Gln
> None None None None Gln
> None None None None Phe
> None None None None Leu
> None None None None Asn
> None None None None Val
> None None None None Val
> None None None None Lys
> None None None None Ile
> None None None None Pro
> None None None None Pro
> None None None None Thr
> None None None None Ile
> None None None None Arg
> None None None None His
> None None None None Ala
> None None None None Leu
> None None None None Gly
> None None None None Phe
> None None None None Met
> None None None None Ser
> None None None None Met
> None None None None His
> None None None None Leu
> None None None None Leu
>
> relax> spectrum.read_intensities(file='T1_0111.list', dir=None, spectrum_id='T1_0111', heteronuc='N', proton='HN', int_method='height', int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, ncproc=None)
> Opening the file 'T1_0111.list' for reading.
> Sparky formatted data file.
>
> Number of header lines found: 1
> RelaxWarning: Cannot find the spin :42@N within the sequence.
> RelaxWarning: Cannot find the spin :79@N within the sequence.
> RelaxWarning: Cannot find the spin :35@N within the sequence.
> RelaxWarning: Cannot find the spin :39@N within the sequence.
> RelaxWarning: Cannot find the spin :80@N within the sequence.
> RelaxWarning: Cannot find the spin :37@N within the sequence.
> RelaxWarning: Cannot find the spin :49@N within the sequence.
> RelaxWarning: Cannot find the spin :20@N within the sequence.
> RelaxWarning: Cannot find the spin :26@N within the sequence.
> RelaxWarning: Cannot find the spin :66@N within the sequence.
> RelaxWarning: Cannot find the spin :30@N within the sequence.
> RelaxWarning: Cannot find the spin :74@N within the sequence.
> RelaxWarning: Cannot find the spin :36@N within the sequence.
> RelaxWarning: Cannot find the spin :83@N within the sequence.
> RelaxWarning: Cannot find the spin :29@N within the sequence.
> RelaxWarning: Cannot find the spin :7@N within the sequence.
> RelaxWarning: Cannot find the spin :31@N within the sequence.
> RelaxWarning: Cannot find the spin :59@N within the sequence.
> RelaxWarning: Cannot find the spin :71@N within the sequence.
> RelaxWarning: Cannot find the spin :13@N within the sequence.
> RelaxWarning: Cannot find the spin :75@N within the sequence.
> RelaxWarning: Cannot find the spin :22@N within the sequence.
> RelaxWarning: Cannot find the spin :68@N within the sequence.
> RelaxWarning: Cannot find the spin :41@N within the sequence.
> RelaxWarning: Cannot find the spin :67@N within the sequence.
> RelaxWarning: Cannot find the spin :52@N within the sequence.
> RelaxWarning: Cannot find the spin :4@N within the sequence.
> RelaxWarning: Cannot find the spin :86@N within the sequence.
> RelaxWarning: Cannot find the spin :10@N within the sequence.
> RelaxWarning: Cannot find the spin :54@N within the sequence.
> RelaxWarning: Cannot find the spin :88@N within the sequence.
> RelaxWarning: Cannot find the spin :34@N within the sequence.
> RelaxWarning: Cannot find the spin :60@N within the sequence.
> RelaxWarning: Cannot find the spin :65@N within the sequence.
> RelaxWarning: Cannot find the spin :57@N within the sequence.
> RelaxWarning: Cannot find the spin :15@N within the sequence.
> RelaxWarning: Cannot find the spin :78@N within the sequence.
> RelaxWarning: Cannot find the spin :84@N within the sequence.
> RelaxWarning: Cannot find the spin :25@N within the sequence.
> RelaxWarning: Cannot find the spin :40@N within the sequence.
> RelaxWarning: Cannot find the spin :56@N within the sequence.
> RelaxWarning: Cannot find the spin :48@N within the sequence.
> RelaxWarning: Cannot find the spin :61@N within the sequence.
> RelaxWarning: Cannot find the spin :12@N within the sequence.
> RelaxWarning: Cannot find the spin :53@N within the sequence.
> RelaxWarning: Cannot find the spin :6@N within the sequence.
> RelaxWarning: Cannot find the spin :43@N within the sequence.
> RelaxWarning: Cannot find the spin :33@N within the sequence.
> RelaxWarning: Cannot find the spin :72@N within the sequence.
> RelaxWarning: Cannot find the spin :32@N within the sequence.
> RelaxWarning: Cannot find the spin :16@N within the sequence.
> RelaxWarning: Cannot find the spin :19@N within the sequence.
> RelaxWarning: Cannot find the spin :11@N within the sequence.
> RelaxWarning: Cannot find the spin :21@N within the sequence.
> RelaxWarning: Cannot find the spin :58@N within the sequence.
> RelaxWarning: Cannot find the spin :8@N within the sequence.
> RelaxWarning: Cannot find the spin :28@N within the sequence.
> RelaxWarning: Cannot find the spin :62@N within the sequence.
> RelaxWarning: Cannot find the spin :45@N within the sequence.
> RelaxWarning: Cannot find the spin :91@N within the sequence.
> RelaxError: No data could be loaded from the peak list
>
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