Re: relax-users Digest, Vol 74, Issue 8 -- September 06, 2012

Cheers!  The column numbering has changed - the reason was that many
users were confused with the concept of counting starting at zero.
There was also a default of the residue number and name columns being
set to the first and second columns as well - this was removed for the
organic chemists who do not have residues, as having default residue
columns caused failures for organic molecules.  So I'm guessing the
script you sent to Nick only had the spin name column set to 2 and the
res_num_col and res_name_col arguments not set.  That would make sense
and would explain the output Nick sees.  Specifying the columns for
this user function should fix this problem, though there might be some
relax version differences later on in the script which will cause more
problems.  The user function documentation should be able to explain
and resolve these issues as well.

Regards,

Edward


On 6 September 2012 21:17, Madeleine Strickland
<M.Strickland@xxxxxxxxxxxxx> wrote:

Hi Nicholas, this data is from a couple of years ago run on red hat
enterprise. The issue here is that column definitions are different, in your
version column 0 doesn't exist. You need to change the sequence line to
this....

sequnce.read('sequence.out', res_num_col=1, res_name_col=2, spin_name_col=3)

I used relax 1.3.9 for this, or earlier, which is why definitions are
slightly different.

Hope this helps.

Maddy

Not sure about the monte carlo errors though!

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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

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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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Re: relax-users Digest, Vol 74, Issue 8

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